rs2142672

Variant names:

• chr6-16196963-G-A
• rs2142672
• ENST00000755734.1:n.516+3632C>T

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. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000755734.1(ENSG00000298476):​n.516+3632C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000298476 ENST00000755734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 24 publications found

Genes affected

ENSG00000298476 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000298476	ENST00000755734.1	n.516+3632C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.692 AC: 28636 AN: 41354

American (AMR) AF: 0.370 AC: 5652 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1070 AN: 3472

East Asian (EAS) AF: 0.737 AC: 3771 AN: 5120

South Asian (SAS) AF: 0.345 AC: 1660 AN: 4812

European-Finnish (FIN) AF: 0.244 AC: 2574 AN: 10554

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18597 AN: 67942

Other (OTH) AF: 0.369 AC: 779 AN: 2110

Alfa AF: 0.321 Hom.: 36624

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2142672; hg19: chr6-16197194;