rs1339844

Variant names:

• chr10-83106913-G-A
• rs1339844

Your query was ambiguous. Multiple possible variants found:

• chr10-83106913-G-A
• chr10-83106913-G-C

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 0.361 in 151,898 control chromosomes in the GnomAD database, including 11,319 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 0.36 (11319 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 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: 0.361 AC: 54852 AN: 151780 Hom.: 11301 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.361 AC: 54907 AN: 151898 Hom.: 11319 Cov.: 32 AF XY: 0.369 AC XY: 27368 AN XY: 74236

African (AFR) AF: 0.503 AC: 20821 AN: 41408

American (AMR) AF: 0.394 AC: 5997 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 974 AN: 3464

East Asian (EAS) AF: 0.746 AC: 3853 AN: 5166

South Asian (SAS) AF: 0.426 AC: 2047 AN: 4800

European-Finnish (FIN) AF: 0.321 AC: 3386 AN: 10558

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16934 AN: 67946

Other (OTH) AF: 0.324 AC: 683 AN: 2110

Alfa AF: 0.284 Hom.: 10980

Bravo AF: 0.373

Asia WGS AF: 0.534 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1339844; hg19: chr10-84866669;