7-127529843-C-T

Variant names:

• chr7-127529843-C-T
• rs10282411
• ENST00000731796.1:n.70-24477G>A

Variant summary

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

The ENST00000731796.1(ENSG00000295686):​n.70-24477G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,954 control chromosomes in the GnomAD database, including 19,387 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 0.47 (19387 hom., cov: 32)
• Consequence: ENSG00000295686 ENST00000731796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 5 publications found

Genes affected

ENSG00000295686 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375490	XR_001745351.2	n.2291+5306G>A		intron_variant	Intron 2 of 4
LOC105375490	XR_001745352.2	n.493+5306G>A		intron_variant	Intron 3 of 5
LOC105375490	XR_007060511.1	n.174+5306G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295686	ENST00000731796.1	n.70-24477G>A		intron_variant	Intron 1 of 2
ENSG00000295686	ENST00000731797.1	n.355-44561G>A		intron_variant	Intron 3 of 3
ENSG00000295686	ENST00000731798.1	n.243+5306G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72072 AN: 151838 Hom.: 19366 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.475 AC: 72114 AN: 151954 Hom.: 19387 Cov.: 32 AF XY: 0.484 AC XY: 35959 AN XY: 74268

African (AFR) AF: 0.235 AC: 9742 AN: 41442

American (AMR) AF: 0.469 AC: 7151 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1213 AN: 3468

East Asian (EAS) AF: 0.878 AC: 4549 AN: 5184

South Asian (SAS) AF: 0.614 AC: 2957 AN: 4816

European-Finnish (FIN) AF: 0.644 AC: 6793 AN: 10544

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.563 AC: 38220 AN: 67930

Other (OTH) AF: 0.450 AC: 951 AN: 2112

Alfa AF: 0.507 Hom.: 2991

Bravo AF: 0.448

Asia WGS AF: 0.684 AC: 2376 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.0
DANN	Benign	0.64
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10282411; hg19: chr7-127169897;