rs2142672

Variant names:

• chr6-16196963-G-A
• rs2142672

Your query was ambiguous. Multiple possible variants found:

• chr6-16196963-G-A
• chr6-16196963-G-C
• chr6-16196963-G-T

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 0.415 in 151,832 control chromosomes in the GnomAD database, including 15,871 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 0.42 (15871 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 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: 0.415 AC: 62979 AN: 151714 Hom.: 15822 Cov.: 31

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.415 AC: 63086 AN: 151832 Hom.: 15871 Cov.: 31 AF XY: 0.412 AC XY: 30569 AN XY: 74216

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.369

Alfa AF: 0.296 Hom.: 12708

Bravo AF: 0.437

Asia WGS AF: 0.590 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2142672; hg19: chr6-16197194;