rs10488630

Variant names:

• chr7-128953894-A-G
• rs10488630

Your query was ambiguous. Multiple possible variants found:

• chr7-128953894-A-G
• chr7-128953894-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 0.273 in 152,160 control chromosomes in the GnomAD database, including 6,938 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 0.27 (6938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 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: 0.273 AC: 41480 AN: 152042 Hom.: 6937 Cov.: 32

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.273 AC: 41479 AN: 152160 Hom.: 6938 Cov.: 32 AF XY: 0.271 AC XY: 20146 AN XY: 74374

African (AFR) AF: 0.0762 AC: 3165 AN: 41540

American (AMR) AF: 0.274 AC: 4193 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1570 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1703 AN: 5176

South Asian (SAS) AF: 0.301 AC: 1452 AN: 4824

European-Finnish (FIN) AF: 0.351 AC: 3704 AN: 10566

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24582 AN: 67976

Other (OTH) AF: 0.304 AC: 641 AN: 2112

Alfa AF: 0.339 Hom.: 8433

Bravo AF: 0.262

Asia WGS AF: 0.304 AC: 1057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.8
DANN	Benign	0.81
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10488630; hg19: chr7-128593948;