ENST00000626400.2:n.131-7917A>C

Variant names:

• chr11-129603795-A-C
• rs7107217
• ENST00000626400.2:n.131-7917A>C

Variant summary

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

The ENST00000626400.2(ENSG00000281386):​n.131-7917A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,066 control chromosomes in the GnomAD database, including 23,069 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 0.55 (23069 hom., cov: 33)
• Consequence: ENSG00000281386 ENST00000626400.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.649
• Publications: 40 publications found

Genes affected

ENSG00000281386 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.614 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
ENSG00000281386	ENST00000626400.2	n.131-7917A>C		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83121 AN: 151948 Hom.: 23059 Cov.: 33

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.547 AC: 83153 AN: 152066 Hom.: 23069 Cov.: 33 AF XY: 0.544 AC XY: 40431 AN XY: 74324

African (AFR) AF: 0.548 AC: 22743 AN: 41472

American (AMR) AF: 0.537 AC: 8209 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2124 AN: 3470

East Asian (EAS) AF: 0.347 AC: 1799 AN: 5182

South Asian (SAS) AF: 0.633 AC: 3049 AN: 4818

European-Finnish (FIN) AF: 0.476 AC: 5023 AN: 10562

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38329 AN: 67970

Other (OTH) AF: 0.555 AC: 1172 AN: 2110

Alfa AF: 0.554 Hom.: 45037

Bravo AF: 0.544

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.83
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs7107217; hg19: chr11-129473690;