13-107870547-A-G

Variant names:

• chr13-107870547-A-G
• rs816958
• ENST00000622038.1:n.165A>G

Variant summary

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

The ENST00000622038.1(ENSG00000274718):​n.165A>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 0.578 in 152,108 control chromosomes in the GnomAD database, including 26,333 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 0.58 (26332 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENSG00000274718 ENST00000622038.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 5 publications found

Genes affected

ENSG00000274718 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000622038.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000274718	ENST00000622038.1	TSL:6	n.165A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000286343	ENST00000663056.1		n.104+1621A>G		intron	N/A
	ENSG00000286343	ENST00000733863.1		n.118+1621A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87861 AN: 151988 Hom.: 26271 Cov.: 33

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.576

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.578 AC: 87991 AN: 152106 Hom.: 26332 Cov.: 33 AF XY: 0.584 AC XY: 43436 AN XY: 74360

African (AFR) AF: 0.727 AC: 30151 AN: 41492

American (AMR) AF: 0.552 AC: 8439 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3468

East Asian (EAS) AF: 0.788 AC: 4067 AN: 5164

South Asian (SAS) AF: 0.624 AC: 3017 AN: 4832

European-Finnish (FIN) AF: 0.556 AC: 5865 AN: 10556

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33015 AN: 67978

Other (OTH) AF: 0.578 AC: 1224 AN: 2116

Alfa AF: 0.520 Hom.: 64924

Bravo AF: 0.587

Asia WGS AF: 0.696 AC: 2419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.1
DANN	Benign	0.25
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs816958; hg19: chr13-108522895;