chr3-57982666-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.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

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 v4.9

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;