rs744103

Variant names:

• chr6-43837625-T-A
• rs744103
• ENST00000637813.1:n.366-4886T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-43837625-T-A
• chr6-43837625-T-C
• chr6-43837625-T-G

Variant summary

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

The ENST00000637813.1(ENSG00000283573):​n.366-4886T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 152,120 control chromosomes in the GnomAD database, including 29,256 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 0.59 (29256 hom., cov: 33)
• Consequence: ENSG00000283573 ENST00000637813.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 16 publications found

Genes affected

ENSG00000283573 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637813.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283573	ENST00000637813.1	TSL:4	n.366-4886T>A		intron	N/A
	ENSG00000283573	ENST00000719551.1		n.193-4886T>A		intron	N/A
	ENSG00000294041	ENST00000720677.1		n.333-268T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90074 AN: 152002 Hom.: 29252 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.592 AC: 90106 AN: 152120 Hom.: 29256 Cov.: 33 AF XY: 0.597 AC XY: 44400 AN XY: 74374

African (AFR) AF: 0.301 AC: 12481 AN: 41452

American (AMR) AF: 0.729 AC: 11143 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2445 AN: 3472

East Asian (EAS) AF: 0.799 AC: 4144 AN: 5186

South Asian (SAS) AF: 0.749 AC: 3614 AN: 4826

European-Finnish (FIN) AF: 0.682 AC: 7226 AN: 10588

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46974 AN: 67984

Other (OTH) AF: 0.609 AC: 1287 AN: 2114

Alfa AF: 0.633 Hom.: 4003

Bravo AF: 0.582

Asia WGS AF: 0.727 AC: 2529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.3
DANN	Benign	0.89
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs744103; hg19: chr6-43805362;