rs1317361

chr10-89119547-A-Gchr10-89119547-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 0.386 in 152,068 control chromosomes in the GnomAD database, including 11,949 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 0.39 (11949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.793

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 = 0.648 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: 0.386 AC: 58715 AN: 151950 Hom.: 11946 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.386 AC: 58734 AN: 152068 Hom.: 11949 Cov.: 32 AF XY: 0.392 AC XY: 29129 AN XY: 74308

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.402

Alfa AF: 0.415 Hom.: 26557

Bravo AF: 0.379

Asia WGS AF: 0.521 AC: 1811 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	5.5
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1317361; hg19: chr10-90879304;