6-160318473-C-T

Variant names:

• chr6-160318473-C-T
• rs415897

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 0.618 in 152,030 control chromosomes in the GnomAD database, including 29,269 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 0.62 (29269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• 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 (NFE) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93831 AN: 151910 Hom.: 29245 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.618 AC: 93900 AN: 152030 Hom.: 29269 Cov.: 32 AF XY: 0.612 AC XY: 45476 AN XY: 74310

African (AFR) AF: 0.588 AC: 24367 AN: 41464

American (AMR) AF: 0.524 AC: 8012 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2111 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2321 AN: 5172

South Asian (SAS) AF: 0.479 AC: 2310 AN: 4820

European-Finnish (FIN) AF: 0.639 AC: 6724 AN: 10528

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46076 AN: 67982

Other (OTH) AF: 0.619 AC: 1304 AN: 2108

Alfa AF: 0.629 Hom.: 5307

Bravo AF: 0.610

Asia WGS AF: 0.456 AC: 1589 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	0.57
DANN	Benign	0.48
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs415897; hg19: chr6-160739505;