chr10-77641558-T-C

Variant names:

• chr10-77641558-T-C
• rs7071206

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 33 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.144 AC: 5992 AN: 41544

American (AMR) AF: 0.194 AC: 2965 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3468

East Asian (EAS) AF: 0.540 AC: 2784 AN: 5160

South Asian (SAS) AF: 0.337 AC: 1624 AN: 4820

European-Finnish (FIN) AF: 0.196 AC: 2082 AN: 10614

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.207 AC: 14083 AN: 68010

Other (OTH) AF: 0.215 AC: 453 AN: 2110

Alfa AF: 0.209 Hom.: 13016

Bravo AF: 0.201

Asia WGS AF: 0.416 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.085
DANN	Benign	0.61
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7071206; hg19: chr10-79401316;