chr7-157297619-T-C

Variant names:

• chr7-157297619-T-C
• rs2527865
• ENST00000728178.1:n.577-148A>G

Variant summary

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

The ENST00000728178.1(ENSG00000295124):​n.577-148A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 152,044 control chromosomes in the GnomAD database, including 15,462 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 0.43 (15462 hom., cov: 33)
• Consequence: ENSG00000295124 ENST00000728178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 4 publications found

Genes affected

ENSG00000295124 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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
ENSG00000295124	ENST00000728178.1	n.577-148A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65957 AN: 151926 Hom.: 15433 Cov.: 33

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.434 AC: 66039 AN: 152044 Hom.: 15462 Cov.: 33 AF XY: 0.441 AC XY: 32808 AN XY: 74328

African (AFR) AF: 0.593 AC: 24592 AN: 41446

American (AMR) AF: 0.477 AC: 7290 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1029 AN: 3472

East Asian (EAS) AF: 0.552 AC: 2854 AN: 5172

South Asian (SAS) AF: 0.400 AC: 1927 AN: 4820

European-Finnish (FIN) AF: 0.458 AC: 4842 AN: 10568

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22144 AN: 67976

Other (OTH) AF: 0.433 AC: 913 AN: 2110

Alfa AF: 0.356 Hom.: 3664

Bravo AF: 0.445

Asia WGS AF: 0.477 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.56
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2527865; hg19: chr7-157090313;