chr6-70664857-C-T

Variant names:

• chr6-70664857-C-T
• rs781978

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 0.434 in 151,964 control chromosomes in the GnomAD database, including 14,670 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 0.43 (14670 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65917 AN: 151848 Hom.: 14671 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.434 AC: 65933 AN: 151964 Hom.: 14670 Cov.: 32 AF XY: 0.432 AC XY: 32079 AN XY: 74256

African (AFR) AF: 0.377 AC: 15601 AN: 41418

American (AMR) AF: 0.420 AC: 6420 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1389 AN: 3468

East Asian (EAS) AF: 0.230 AC: 1187 AN: 5162

South Asian (SAS) AF: 0.496 AC: 2389 AN: 4820

European-Finnish (FIN) AF: 0.444 AC: 4679 AN: 10538

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32728 AN: 67964

Other (OTH) AF: 0.457 AC: 963 AN: 2108

Alfa AF: 0.448 Hom.: 2311

Bravo AF: 0.424

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.031
DANN	Benign	0.68
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs781978; hg19: chr6-71374560;