rs1231339

Variant names:

• chr9-25740865-A-C
• rs1231339

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 0.525 in 151,904 control chromosomes in the GnomAD database, including 21,115 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 0.53 (21115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.551 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: 0.525 AC: 79750 AN: 151786 Hom.: 21091 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.525 AC: 79816 AN: 151904 Hom.: 21115 Cov.: 32 AF XY: 0.524 AC XY: 38894 AN XY: 74272

African (AFR) AF: 0.557 AC: 23068 AN: 41394

American (AMR) AF: 0.469 AC: 7143 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2294 AN: 3466

East Asian (EAS) AF: 0.525 AC: 2711 AN: 5168

South Asian (SAS) AF: 0.566 AC: 2729 AN: 4822

European-Finnish (FIN) AF: 0.471 AC: 4985 AN: 10576

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35088 AN: 67918

Other (OTH) AF: 0.540 AC: 1139 AN: 2110

Alfa AF: 0.522 Hom.: 26823

Bravo AF: 0.521

Asia WGS AF: 0.540 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.70
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1231339; hg19: chr9-25740863;