10-107320676-T-C

Variant names:

• chr10-107320676-T-C
• rs10509832

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 0.44 in 152,082 control chromosomes in the GnomAD database, including 17,228 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 0.44 (17228 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66898 AN: 151964 Hom.: 17228 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.440 AC: 66907 AN: 152082 Hom.: 17228 Cov.: 32 AF XY: 0.438 AC XY: 32543 AN XY: 74346

African (AFR) AF: 0.157 AC: 6504 AN: 41512

American (AMR) AF: 0.468 AC: 7150 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1937 AN: 3468

East Asian (EAS) AF: 0.415 AC: 2143 AN: 5166

South Asian (SAS) AF: 0.453 AC: 2186 AN: 4822

European-Finnish (FIN) AF: 0.509 AC: 5373 AN: 10560

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39905 AN: 67968

Other (OTH) AF: 0.465 AC: 981 AN: 2110

Alfa AF: 0.532 Hom.: 16992

Bravo AF: 0.423

Asia WGS AF: 0.368 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.37
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs10509832; hg19: chr10-109080434;