rs2527866

Variant names:

• chr7-157297602-C-A
• rs2527866
• ENST00000728178.1:n.577-131G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-157297602-C-A
• chr7-157297602-C-G
• chr7-157297602-C-T

Variant summary

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

The ENST00000728178.1(ENSG00000295124):​n.577-131G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,034 control chromosomes in the GnomAD database, including 10,692 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 0.37 (10692 hom., cov: 33)
• Consequence: ENSG00000295124 ENST00000728178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 19 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000728178.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295124	ENST00000728178.1		n.577-131G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56066 AN: 151916 Hom.: 10681 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.369 AC: 56108 AN: 152034 Hom.: 10692 Cov.: 33 AF XY: 0.379 AC XY: 28166 AN XY: 74330

African (AFR) AF: 0.386 AC: 16016 AN: 41468

American (AMR) AF: 0.444 AC: 6776 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3468

East Asian (EAS) AF: 0.529 AC: 2735 AN: 5172

South Asian (SAS) AF: 0.354 AC: 1709 AN: 4828

European-Finnish (FIN) AF: 0.459 AC: 4836 AN: 10544

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21922 AN: 67974

Other (OTH) AF: 0.372 AC: 784 AN: 2106

Alfa AF: 0.344 Hom.: 27046

Bravo AF: 0.369

Asia WGS AF: 0.429 AC: 1486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.66
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2527866; hg19: chr7-157090296;