rs2675663

Variant names:

• chr10-73900512-T-G
• rs2675663

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 0.422 in 151,972 control chromosomes in the GnomAD database, including 15,159 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 0.42 (15159 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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: 0.422 AC: 64059 AN: 151854 Hom.: 15157 Cov.: 31

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.422 AC: 64068 AN: 151972 Hom.: 15159 Cov.: 31 AF XY: 0.416 AC XY: 30876 AN XY: 74260

African (AFR) AF: 0.241 AC: 9970 AN: 41446

American (AMR) AF: 0.423 AC: 6458 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1896 AN: 3470

East Asian (EAS) AF: 0.109 AC: 563 AN: 5178

South Asian (SAS) AF: 0.276 AC: 1327 AN: 4814

European-Finnish (FIN) AF: 0.466 AC: 4889 AN: 10502

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37296 AN: 67978

Other (OTH) AF: 0.490 AC: 1029 AN: 2102

Alfa AF: 0.456 Hom.: 2207

Bravo AF: 0.413

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs2675663; hg19: chr10-75660270;