rs1326663

Variant names:

• chr10-120420014-A-G
• rs1326663

Your query was ambiguous. Multiple possible variants found:

• chr10-120420014-A-G
• chr10-120420014-A-T

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 0.309 in 150,082 control chromosomes in the GnomAD database, including 8,917 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 0.31 (8917 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 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: 0.308 AC: 46259 AN: 149970 Hom.: 8887 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.309 AC: 46331 AN: 150082 Hom.: 8917 Cov.: 32 AF XY: 0.311 AC XY: 22808 AN XY: 73350

African (AFR) AF: 0.566 AC: 22661 AN: 40044

American (AMR) AF: 0.216 AC: 3284 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 456 AN: 3450

East Asian (EAS) AF: 0.332 AC: 1656 AN: 4984

South Asian (SAS) AF: 0.298 AC: 1412 AN: 4732

European-Finnish (FIN) AF: 0.280 AC: 2939 AN: 10510

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.194 AC: 13190 AN: 67854

Other (OTH) AF: 0.261 AC: 547 AN: 2096

Alfa AF: 0.261 Hom.: 2568

Bravo AF: 0.308

Asia WGS AF: 0.324 AC: 1124 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.096
DANN	Benign	0.38
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs1326663; hg19: chr10-122179526;