rs10488360

chr7-4371578-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.339

Alfa AF: 0.316 Hom.: 17759

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488360; hg19: chr7-4411209;