rs10510677

Variant names:

• chr3-36151574-A-G
• rs10510677

Your query was ambiguous. Multiple possible variants found:

• chr3-36151574-A-G
• chr3-36151574-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 0.287 in 151,970 control chromosomes in the GnomAD database, including 6,488 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 0.29 (6488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

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 (EAS) allele frequency at 95% confidence interval = 0.382 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: 0.287 AC: 43557 AN: 151850 Hom.: 6476 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.287 AC: 43614 AN: 151970 Hom.: 6488 Cov.: 32 AF XY: 0.295 AC XY: 21910 AN XY: 74288

African (AFR) AF: 0.312 AC: 12918 AN: 41446

American (AMR) AF: 0.297 AC: 4541 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3472

East Asian (EAS) AF: 0.396 AC: 2039 AN: 5148

South Asian (SAS) AF: 0.235 AC: 1133 AN: 4822

European-Finnish (FIN) AF: 0.396 AC: 4177 AN: 10558

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17086 AN: 67950

Other (OTH) AF: 0.277 AC: 583 AN: 2106

Alfa AF: 0.257 Hom.: 2957

Bravo AF: 0.280

Asia WGS AF: 0.318 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.8
DANN	Benign	0.58
PhyloP100		-0.0090

Splicing

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

Publications

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Other links and lift over

dbSNP: rs10510677; hg19: chr3-36193066;