10-77641558-T-C

Variant names:

• chr10-77641558-T-C
• rs7071206

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 0.204 in 152,222 control chromosomes in the GnomAD database, including 3,686 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 0.20 (3686 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 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: 0.204 AC: 31049 AN: 152104 Hom.: 3681 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.204 AC: 31062 AN: 152222 Hom.: 3686 Cov.: 33 AF XY: 0.206 AC XY: 15359 AN XY: 74416

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.215

Alfa AF: 0.203 Hom.: 3980

Bravo AF: 0.201

Asia WGS AF: 0.416 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.085
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7071206; hg19: chr10-79401316;