rs1194670

Variant names:

• chr10-52388284-A-C
• rs1194670

Your query was ambiguous. Multiple possible variants found:

• chr10-52388284-A-C
• chr10-52388284-A-G
• chr10-52388284-A-T

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 0.714 in 152,128 control chromosomes in the GnomAD database, including 40,238 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 0.71 (40238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 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: 0.714 AC: 108505 AN: 152010 Hom.: 40169 Cov.: 32

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.714 AC: 108632 AN: 152128 Hom.: 40238 Cov.: 32 AF XY: 0.711 AC XY: 52892 AN XY: 74360

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.667

Alfa AF: 0.617 Hom.: 3517

Bravo AF: 0.723

Asia WGS AF: 0.837 AC: 2906 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1194670; hg19: chr10-54148044;