1-37317273-A-G

Variant names:

• chr1-37317273-A-G
• rs1411931
• ENST00000413901.1:n.111+7717T>C

Variant summary

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

The ENST00000413901.1(ENSG00000223944):​n.111+7717T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,062 control chromosomes in the GnomAD database, including 32,877 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 0.65 (32877 hom., cov: 32)
• Consequence: ENSG00000223944 ENST00000413901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 7 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413901.1. 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
	ENSG00000223944	ENST00000413901.1	TSL:3	n.111+7717T>C		intron	N/A
	ENSG00000223944	ENST00000655056.1		n.324+1047T>C		intron	N/A
	ENSG00000223944	ENST00000702690.2		n.334+1047T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98635 AN: 151944 Hom.: 32862 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.649 AC: 98686 AN: 152062 Hom.: 32877 Cov.: 32 AF XY: 0.655 AC XY: 48738 AN XY: 74376

African (AFR) AF: 0.520 AC: 21565 AN: 41436

American (AMR) AF: 0.748 AC: 11432 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2346 AN: 3472

East Asian (EAS) AF: 0.963 AC: 4973 AN: 5164

South Asian (SAS) AF: 0.611 AC: 2947 AN: 4820

European-Finnish (FIN) AF: 0.748 AC: 7925 AN: 10592

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45291 AN: 67970

Other (OTH) AF: 0.659 AC: 1393 AN: 2114

Alfa AF: 0.649 Hom.: 39319

Bravo AF: 0.649

Asia WGS AF: 0.764 AC: 2654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.5
DANN	Benign	0.86
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs1411931; hg19: chr1-37782874;