chr6-164164642-G-T

Variant names:

• chr6-164164642-G-T
• rs2764649

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 0.323 in 152,006 control chromosomes in the GnomAD database, including 9,625 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 0.32 (9625 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 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: 0.323 AC: 48984 AN: 151888 Hom.: 9602 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.323 AC: 49064 AN: 152006 Hom.: 9625 Cov.: 32 AF XY: 0.324 AC XY: 24049 AN XY: 74310

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.305

Alfa AF: 0.314 Hom.: 1329

Bravo AF: 0.331

Asia WGS AF: 0.386 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.55
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2764649; hg19: chr6-164585674;