rs2544208

Variant names:

• chr7-134285364-C-A
• rs2544208
• ENST00000420268.1:n.215-492C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-134285364-C-A
• chr7-134285364-C-G
• chr7-134285364-C-T

Variant summary

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

The ENST00000420268.1(ENSG00000231098):​n.215-492C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,176 control chromosomes in the GnomAD database, including 2,918 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 0.12 (2918 hom., cov: 33)
• Consequence: ENSG00000231098 ENST00000420268.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748
• Publications: 1 publications found

Genes affected

ENSG00000231098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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
ENSG00000231098	ENST00000420268.1	n.215-492C>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18870 AN: 152058 Hom.: 2897 Cov.: 33

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0698

Gnomad FIN AF: 0.0345

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0148

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.124 AC: 18942 AN: 152176 Hom.: 2918 Cov.: 33 AF XY: 0.123 AC XY: 9137 AN XY: 74400

African (AFR) AF: 0.360 AC: 14910 AN: 41470

American (AMR) AF: 0.0743 AC: 1137 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3470

East Asian (EAS) AF: 0.138 AC: 713 AN: 5180

South Asian (SAS) AF: 0.0696 AC: 336 AN: 4826

European-Finnish (FIN) AF: 0.0345 AC: 366 AN: 10610

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0148 AC: 1005 AN: 68002

Other (OTH) AF: 0.104 AC: 219 AN: 2114

Alfa AF: 0.0498 Hom.: 146

Bravo AF: 0.139

Asia WGS AF: 0.115 AC: 400 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	0.14
DANN	Benign	0.43
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs2544208; hg19: chr7-133970116;