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. Variant got -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

Genes affected

ENSG00000231098 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.0743

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0696

Gnomad4 FIN AF: 0.0345

Gnomad4 NFE AF: 0.0148

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0395 Hom.: 94

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2544208; hg19: chr7-133970116;