rs2867161

Variant names:

• chr7-68172355-C-A
• rs2867161
• ENST00000446187.2:n.465+12435G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-68172355-C-A
• chr7-68172355-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446187.2(ENSG00000226829):​n.465+12435G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,076 control chromosomes in the GnomAD database, including 1,005 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 0.11 (1005 hom., cov: 32)
• Consequence: ENSG00000226829 ENST00000446187.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 3 publications found

Genes affected

ENSG00000226829 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375341	NR_187905.1	n.523+12435G>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226829	ENST00000446187.2	n.465+12435G>T		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17097 AN: 151958 Hom.: 995 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.0649

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0966

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.113 AC: 17144 AN: 152076 Hom.: 1005 Cov.: 32 AF XY: 0.114 AC XY: 8481 AN XY: 74346

African (AFR) AF: 0.155 AC: 6438 AN: 41448

American (AMR) AF: 0.0774 AC: 1182 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3472

East Asian (EAS) AF: 0.0649 AC: 336 AN: 5180

South Asian (SAS) AF: 0.146 AC: 702 AN: 4816

European-Finnish (FIN) AF: 0.117 AC: 1240 AN: 10588

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0966 AC: 6567 AN: 67990

Other (OTH) AF: 0.113 AC: 237 AN: 2098

Alfa AF: 0.0946 Hom.: 1175

Bravo AF: 0.110

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.014
DANN	Benign	0.37
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2867161; hg19: chr7-67637342;