6-164179816-C-T

Variant names:

• chr6-164179816-C-T
• rs1894638

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.395 in 152,002 control chromosomes in the GnomAD database, including 13,753 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 0.40 (13753 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60081 AN: 151884 Hom.: 13751 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.395 AC: 60089 AN: 152002 Hom.: 13753 Cov.: 32 AF XY: 0.403 AC XY: 29913 AN XY: 74294

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.454

Alfa AF: 0.306 Hom.: 1337

Bravo AF: 0.382

Asia WGS AF: 0.341 AC: 1187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.56
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1894638; hg19: chr6-164600848;