rs10488360

Variant names:

• chr7-4371578-G-A
• rs10488360

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 0.319 in 150,850 control chromosomes in the GnomAD database, including 7,825 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 0.32 (7825 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 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: 0.319 AC: 48095 AN: 150768 Hom.: 7812 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.319 AC: 48139 AN: 150850 Hom.: 7825 Cov.: 32 AF XY: 0.324 AC XY: 23790 AN XY: 73524

African (AFR) AF: 0.314 AC: 12921 AN: 41172

American (AMR) AF: 0.389 AC: 5905 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1244 AN: 3466

East Asian (EAS) AF: 0.430 AC: 2209 AN: 5140

South Asian (SAS) AF: 0.363 AC: 1742 AN: 4804

European-Finnish (FIN) AF: 0.281 AC: 2817 AN: 10016

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20225 AN: 67768

Other (OTH) AF: 0.339 AC: 709 AN: 2094

Alfa AF: 0.314 Hom.: 34465

Bravo AF: 0.330

Asia WGS AF: 0.350 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.38
PhyloP100		-0.0010

Splicing

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

Other links and lift over

dbSNP: rs10488360; hg19: chr7-4411209;