1-156199819-A-G

Variant names:

• chr1-156199819-A-G
• rs2072499
• ENST00000469537.1:n.3615A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000469537.1(SLC25A44):​n.3615A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 1,595,982 control chromosomes in the GnomAD database, including 105,876 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.42 (14916 hom., cov: 31)
  • Exomes 𝑓: 0.35 (90960 hom.)
• Consequence: SLC25A44 ENST00000469537.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 47 publications found

Genes affected

SLC25A44 (HGNC:29036): (solute carrier family 25 member 44) SLC25A44 belongs to the SLC25 family of mitochondrial carrier proteins (Haitina et al., 2006 [PubMed 16949250]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000469537.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A44	NM_014655.4	MANE Select	c.-13-16A>G		intron	N/A	NP_055470.1
	SLC25A44	NM_001286184.2		c.-13-16A>G		intron	N/A	NP_001273113.1
	SLC25A44	NM_001377385.1		c.-13-16A>G		intron	N/A	NP_001364314.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A44	ENST00000469537.1	TSL:1	n.3615A>G		non_coding_transcript_exon	Exon 1 of 3
	SLC25A44	ENST00000359511.5	TSL:1 MANE Select	c.-13-16A>G		intron	N/A	ENSP00000352497.4
	SLC25A44	ENST00000423538.6	TSL:1	c.-13-16A>G		intron	N/A	ENSP00000407560.3

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63752 AN: 151800 Hom.: 14873 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.404

GnomAD2 exomes AF: 0.336 AC: 80107 AN: 238738 AF XY: 0.331

Gnomad AFR exome AF: 0.644

Gnomad AMR exome AF: 0.286

Gnomad ASJ exome AF: 0.294

Gnomad EAS exome AF: 0.152

Gnomad FIN exome AF: 0.342

Gnomad NFE exome AF: 0.349

Gnomad OTH exome AF: 0.338

GnomAD4 exome AF: 0.349 AC: 503827 AN: 1444064 Hom.: 90960 Cov.: 32 AF XY: 0.346 AC XY: 248084 AN XY: 716980

African (AFR) AF: 0.648 AC: 21550 AN: 33252

American (AMR) AF: 0.294 AC: 12943 AN: 44022

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 7315 AN: 24754

East Asian (EAS) AF: 0.160 AC: 6334 AN: 39622

South Asian (SAS) AF: 0.297 AC: 24674 AN: 83216

European-Finnish (FIN) AF: 0.340 AC: 17814 AN: 52466

Middle Eastern (MID) AF: 0.344 AC: 1948 AN: 5666

European-Non Finnish (NFE) AF: 0.354 AC: 390065 AN: 1101318

Other (OTH) AF: 0.355 AC: 21184 AN: 59748

GnomAD4 genome AF: 0.420 AC: 63843 AN: 151918 Hom.: 14916 Cov.: 31 AF XY: 0.413 AC XY: 30686 AN XY: 74254

African (AFR) AF: 0.633 AC: 26227 AN: 41408

American (AMR) AF: 0.338 AC: 5154 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1045 AN: 3466

East Asian (EAS) AF: 0.159 AC: 822 AN: 5164

South Asian (SAS) AF: 0.288 AC: 1388 AN: 4814

European-Finnish (FIN) AF: 0.349 AC: 3690 AN: 10568

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24283 AN: 67918

Other (OTH) AF: 0.400 AC: 842 AN: 2106

Alfa AF: 0.369 Hom.: 48857

Bravo AF: 0.427

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.36
DANN	Benign	0.37
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2072499; hg19: chr1-156169610;