rs10488183

Variant names:

• chr7-42283933-T-C
• rs10488183

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 0.0915 in 152,276 control chromosomes in the GnomAD database, including 782 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 0.091 (782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.712
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.132 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: 0.0916 AC: 13940 AN: 152158 Hom.: 783 Cov.: 32

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.0308

Gnomad SAS AF: 0.0489

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0915 AC: 13932 AN: 152276 Hom.: 782 Cov.: 32 AF XY: 0.0911 AC XY: 6783 AN XY: 74456

African (AFR) AF: 0.0243 AC: 1012 AN: 41570

American (AMR) AF: 0.137 AC: 2100 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0757 AC: 263 AN: 3472

East Asian (EAS) AF: 0.0309 AC: 160 AN: 5182

South Asian (SAS) AF: 0.0479 AC: 231 AN: 4826

European-Finnish (FIN) AF: 0.120 AC: 1275 AN: 10602

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8592 AN: 68010

Other (OTH) AF: 0.102 AC: 216 AN: 2116

Alfa AF: 0.115 Hom.: 1346

Bravo AF: 0.0903

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.4
DANN	Benign	0.61
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs10488183; hg19: chr7-42323532;