7-50230418-C-T

Variant names:

• chr7-50230418-C-T
• rs2124799
• ENST00000639870.1:n.215-26352G>A

Variant summary

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

The ENST00000639870.1(ENSG00000231681):​n.215-26352G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 151,942 control chromosomes in the GnomAD database, including 36,884 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 0.69 (36884 hom., cov: 32)
• Consequence: ENSG00000231681 ENST00000639870.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 9 publications found

Genes affected

ENSG00000231681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.798 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
ENSG00000231681	ENST00000639870.1	n.215-26352G>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105231 AN: 151824 Hom.: 36847 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.693 AC: 105318 AN: 151942 Hom.: 36884 Cov.: 32 AF XY: 0.697 AC XY: 51736 AN XY: 74258

African (AFR) AF: 0.673 AC: 27891 AN: 41416

American (AMR) AF: 0.765 AC: 11665 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2447 AN: 3468

East Asian (EAS) AF: 0.401 AC: 2068 AN: 5156

South Asian (SAS) AF: 0.819 AC: 3942 AN: 4812

European-Finnish (FIN) AF: 0.727 AC: 7659 AN: 10540

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47474 AN: 67978

Other (OTH) AF: 0.678 AC: 1432 AN: 2112

Alfa AF: 0.698 Hom.: 23545

Bravo AF: 0.684

Asia WGS AF: 0.691 AC: 2390 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.97
DANN	Benign	0.37
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2124799; hg19: chr7-50270014;