3-57982666-A-T

Variant names:

• chr3-57982666-A-T
• rs7637505
• XR_940874.3:n.773-1679A>T

Variant summary

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

The XR_940874.3(LOC105377104):​n.773-1679A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,884 control chromosomes in the GnomAD database, including 11,340 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 0.37 (11340 hom., cov: 32)
• Consequence: LOC105377104 XR_940874.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 2 publications found

Genes affected

LOC105377104 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377104	XR_940874.3	n.773-1679A>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56607 AN: 151768 Hom.: 11311 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.373 AC: 56674 AN: 151884 Hom.: 11340 Cov.: 32 AF XY: 0.372 AC XY: 27597 AN XY: 74234

African (AFR) AF: 0.524 AC: 21701 AN: 41412

American (AMR) AF: 0.303 AC: 4626 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1425 AN: 3466

East Asian (EAS) AF: 0.319 AC: 1639 AN: 5130

South Asian (SAS) AF: 0.310 AC: 1487 AN: 4804

European-Finnish (FIN) AF: 0.363 AC: 3830 AN: 10552

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20871 AN: 67942

Other (OTH) AF: 0.379 AC: 800 AN: 2112

Alfa AF: 0.184 Hom.: 333

Bravo AF: 0.379

Asia WGS AF: 0.350 AC: 1217 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.035
DANN	Benign	0.55
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7637505; hg19: chr3-57968393;