rs2524976

Variant names:

• chr7-96428028-T-C
• rs2524976
• ENST00000768828.1:n.512-392T>C

Variant summary

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

The ENST00000768828.1(ENSG00000300102):​n.512-392T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,102 control chromosomes in the GnomAD database, including 8,171 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 0.32 (8171 hom., cov: 32)
• Consequence: ENSG00000300102 ENST00000768828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548
• Publications: 1 publications found

Genes affected

ENSG00000300102 (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 (NFE) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000768828.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300102	ENST00000768828.1		n.512-392T>C		intron	N/A
	ENSG00000300102	ENST00000768830.1		n.139-650T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48937 AN: 151984 Hom.: 8166 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.0484

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.322 AC: 48974 AN: 152102 Hom.: 8171 Cov.: 32 AF XY: 0.317 AC XY: 23564 AN XY: 74364

African (AFR) AF: 0.334 AC: 13869 AN: 41480

American (AMR) AF: 0.263 AC: 4019 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3470

East Asian (EAS) AF: 0.0485 AC: 251 AN: 5170

South Asian (SAS) AF: 0.230 AC: 1110 AN: 4832

European-Finnish (FIN) AF: 0.366 AC: 3868 AN: 10576

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23685 AN: 67972

Other (OTH) AF: 0.316 AC: 668 AN: 2112

Alfa AF: 0.328 Hom.: 2129

Bravo AF: 0.317

Asia WGS AF: 0.145 AC: 505 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	0.49
DANN	Benign	0.22
PhyloP100		-0.55

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2524976;

hg19: chr7-96057340;