6-153945602-T-C

Variant names:

• chr6-153945602-T-C
• rs7745892

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 0.439 in 151,968 control chromosomes in the GnomAD database, including 15,012 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 0.44 (15012 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 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: 0.439 AC: 66705 AN: 151850 Hom.: 14983 Cov.: 31

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.439 AC: 66774 AN: 151968 Hom.: 15012 Cov.: 31 AF XY: 0.443 AC XY: 32879 AN XY: 74284

African (AFR) AF: 0.520 AC: 21526 AN: 41414

American (AMR) AF: 0.512 AC: 7821 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3472

East Asian (EAS) AF: 0.561 AC: 2895 AN: 5158

South Asian (SAS) AF: 0.506 AC: 2443 AN: 4824

European-Finnish (FIN) AF: 0.357 AC: 3775 AN: 10562

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25256 AN: 67956

Other (OTH) AF: 0.439 AC: 929 AN: 2114

Alfa AF: 0.394 Hom.: 50721

Bravo AF: 0.449

Asia WGS AF: 0.577 AC: 2004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.37
PhyloP100		-0.065

Splicing

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

Other links and lift over

dbSNP: rs7745892; hg19: chr6-154266737;