rs79965208

chr10-62977815-T-Achr10-62977815-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 (7097 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.49 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: 0.389 AC: 38669 AN: 99530 Hom.: 7098 Cov.: 19

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.428

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.388 AC: 38676 AN: 99594 Hom.: 7097 Cov.: 19 AF XY: 0.389 AC XY: 18777 AN XY: 48326

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.413

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.38
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs79965208; hg19: chr10-64737575; COSMIC: COSV55986703;