rs2544208

chr7-134285364-C-Achr7-134285364-C-Gchr7-134285364-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, non coding transcript 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: ENST00000420268.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000420268.1	n.215-492C>A		intron_variant, non_coding_transcript_variant		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;