chr6-163401264-C-T

Variant names:

• chr6-163401264-C-T
• rs4263561

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 0.356 in 152,140 control chromosomes in the GnomAD database, including 11,301 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 0.36 (11301 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 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: 0.356 AC: 54134 AN: 152020 Hom.: 11296 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.356 AC: 54152 AN: 152140 Hom.: 11301 Cov.: 33 AF XY: 0.363 AC XY: 27029 AN XY: 74388

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.367

Alfa AF: 0.378 Hom.: 4964

Bravo AF: 0.331

Asia WGS AF: 0.574 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.77
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4263561; hg19: chr6-163822296; COSMIC: COSV69432263;