rs2080161

Variant names:

• chr7-13291525-A-C
• rs2080161
• ENST00000411542.1:n.237-18684A>C

Your query was ambiguous. Multiple possible variants found:

• chr7-13291525-A-C
• chr7-13291525-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000411542.1(ENSG00000229618):​n.237-18684A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 149,920 control chromosomes in the GnomAD database, including 3,836 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 0.20 (3836 hom., cov: 30)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.393 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
ENSG00000229618	ENST00000411542.1	n.237-18684A>C		intron_variant	Intron 2 of 4	4
ENSG00000229618	ENST00000638964.1	n.609-18684A>C		intron_variant	Intron 2 of 5	5
ENSG00000229618	ENST00000639998.1	n.608-18684A>C		intron_variant	Intron 4 of 7	5

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29409 AN: 149824 Hom.: 3823 Cov.: 30

Gnomad AFR AF: 0.0669

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.196 AC: 29441 AN: 149920 Hom.: 3836 Cov.: 30 AF XY: 0.204 AC XY: 14916 AN XY: 73126

Gnomad4 AFR AF: 0.0669

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.202

Alfa AF: 0.207 Hom.: 4245

Bravo AF: 0.205

Asia WGS AF: 0.243 AC: 839 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.37
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2080161; hg19: chr7-13331150;