chr6-78675752-C-T

Variant names:

• chr6-78675752-C-T
• rs1938551

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 0.793 in 152,100 control chromosomes in the GnomAD database, including 48,012 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 0.79 (48012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.856 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: 0.793 AC: 120515 AN: 151982 Hom.: 47967 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.793 AC: 120621 AN: 152100 Hom.: 48012 Cov.: 32 AF XY: 0.790 AC XY: 58750 AN XY: 74364

African (AFR) AF: 0.810 AC: 33590 AN: 41478

American (AMR) AF: 0.790 AC: 12082 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2975 AN: 3468

East Asian (EAS) AF: 0.843 AC: 4355 AN: 5166

South Asian (SAS) AF: 0.878 AC: 4232 AN: 4820

European-Finnish (FIN) AF: 0.716 AC: 7568 AN: 10564

Middle Eastern (MID) AF: 0.825 AC: 241 AN: 292

European-Non Finnish (NFE) AF: 0.781 AC: 53071 AN: 67990

Other (OTH) AF: 0.787 AC: 1658 AN: 2108

Alfa AF: 0.781 Hom.: 9185

Bravo AF: 0.798

Asia WGS AF: 0.867 AC: 3016 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	1.1
DANN	Benign	0.25
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1938551; hg19: chr6-79385469;