chr4-12486575-G-A

Variant names:

• chr4-12486575-G-A
• rs4437278
• ENST00000808832.1:n.164-15845C>T

Variant summary

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

The ENST00000808832.1(ENSG00000305112):​n.164-15845C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 151,864 control chromosomes in the GnomAD database, including 2,194 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 0.16 (2194 hom., cov: 32)
• Consequence: ENSG00000305112 ENST00000808832.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 3 publications found

Genes affected

ENSG00000305112 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374492	XR_001741374.1	n.255-15845C>T		intron_variant	Intron 1 of 2
LOC105374492	XR_001741375.1	n.676-15845C>T		intron_variant	Intron 1 of 2
LOC105374492	XR_925406.4	n.478-15845C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305112	ENST00000808832.1	n.164-15845C>T		intron_variant	Intron 1 of 3
ENSG00000305112	ENST00000808833.1	n.348-15845C>T		intron_variant	Intron 1 of 3
ENSG00000305112	ENST00000808834.1	n.264-15845C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24168 AN: 151746 Hom.: 2192 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0614

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.205

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.159 AC: 24191 AN: 151864 Hom.: 2194 Cov.: 32 AF XY: 0.155 AC XY: 11483 AN XY: 74200

African (AFR) AF: 0.239 AC: 9909 AN: 41402

American (AMR) AF: 0.159 AC: 2425 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3466

East Asian (EAS) AF: 0.128 AC: 652 AN: 5104

South Asian (SAS) AF: 0.107 AC: 516 AN: 4818

European-Finnish (FIN) AF: 0.0614 AC: 649 AN: 10576

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8874 AN: 67932

Other (OTH) AF: 0.207 AC: 437 AN: 2112

Alfa AF: 0.138 Hom.: 995

Bravo AF: 0.172

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.2
DANN	Benign	0.86
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs4437278; hg19: chr4-12488199;