7-54911231-C-T

Variant names:

• chr7-54911231-C-T
• rs2252586
• ENST00000795375.1:n.164-23898G>A

Variant summary

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

The ENST00000795375.1(ENSG00000303536):​n.164-23898G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,116 control chromosomes in the GnomAD database, including 5,743 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 0.27 (5743 hom., cov: 33)
• Consequence: ENSG00000303536 ENST00000795375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 55 publications found

Genes affected

ENSG00000303536 (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 (NFE) allele frequency at 95% confidence interval = 0.288 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
ENSG00000303536	ENST00000795375.1	n.164-23898G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40530 AN: 151998 Hom.: 5738 Cov.: 33

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.267 AC: 40550 AN: 152116 Hom.: 5743 Cov.: 33 AF XY: 0.261 AC XY: 19379 AN XY: 74364

African (AFR) AF: 0.290 AC: 12008 AN: 41476

American (AMR) AF: 0.223 AC: 3403 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3470

East Asian (EAS) AF: 0.0201 AC: 104 AN: 5186

South Asian (SAS) AF: 0.175 AC: 844 AN: 4828

European-Finnish (FIN) AF: 0.233 AC: 2464 AN: 10574

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19785 AN: 67974

Other (OTH) AF: 0.294 AC: 621 AN: 2114

Alfa AF: 0.279 Hom.: 22788

Bravo AF: 0.266

Asia WGS AF: 0.0930 AC: 323 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	0.019
DANN	Benign	0.68
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2252586; hg19: chr7-54978924;