rs1338864

Variant names:

• chr10-101083466-G-A
• rs1338864

Variant summary

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

The variant allele was found at a frequency of 0.319 in 152,008 control chromosomes in the GnomAD database, including 7,888 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 0.32 (7888 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950
• Publications: 0 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.352 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

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48413 AN: 151890 Hom.: 7888 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.319 AC: 48417 AN: 152008 Hom.: 7888 Cov.: 31 AF XY: 0.315 AC XY: 23373 AN XY: 74316

African (AFR) AF: 0.347 AC: 14375 AN: 41428

American (AMR) AF: 0.319 AC: 4865 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1393 AN: 3472

East Asian (EAS) AF: 0.365 AC: 1886 AN: 5162

South Asian (SAS) AF: 0.317 AC: 1528 AN: 4818

European-Finnish (FIN) AF: 0.216 AC: 2282 AN: 10574

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21024 AN: 67974

Other (OTH) AF: 0.345 AC: 728 AN: 2110

Alfa AF: 0.311 Hom.: 913

Bravo AF: 0.328

Asia WGS AF: 0.363 AC: 1261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.091
DANN	Benign	0.28
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs1338864; hg19: chr10-102843223;