chr1-37257477-A-G

Variant names:

• chr1-37257477-A-G
• rs1501540
• ENST00000655056.1:n.593+12979T>C

Variant summary

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

The ENST00000655056.1(ENSG00000223944):​n.593+12979T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 151,930 control chromosomes in the GnomAD database, including 29,482 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 0.62 (29482 hom., cov: 31)
• Consequence: ENSG00000223944 ENST00000655056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 8 publications found

Genes affected

ENSG00000223944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223944	ENST00000655056.1	n.593+12979T>C		intron_variant	Intron 3 of 3
ENSG00000223944	ENST00000657513.1	n.257+12979T>C		intron_variant	Intron 2 of 3
ENSG00000223944	ENST00000818266.1	n.465+18661T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93644 AN: 151812 Hom.: 29464 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.617 AC: 93700 AN: 151930 Hom.: 29482 Cov.: 31 AF XY: 0.624 AC XY: 46325 AN XY: 74252

African (AFR) AF: 0.556 AC: 23016 AN: 41378

American (AMR) AF: 0.721 AC: 11004 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2245 AN: 3472

East Asian (EAS) AF: 0.965 AC: 4994 AN: 5176

South Asian (SAS) AF: 0.648 AC: 3110 AN: 4798

European-Finnish (FIN) AF: 0.664 AC: 7007 AN: 10554

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40394 AN: 67970

Other (OTH) AF: 0.622 AC: 1311 AN: 2108

Alfa AF: 0.626 Hom.: 5123

Bravo AF: 0.622

Asia WGS AF: 0.774 AC: 2688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.87
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1501540; hg19: chr1-37723078;