2-218145423-C-T

Variant names:

• chr2-218145423-C-T
• rs11676348
• ENST00000811769.1:n.66-5447G>A

Variant summary

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

The ENST00000811769.1(ENSG00000305582):​n.66-5447G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,982 control chromosomes in the GnomAD database, including 21,162 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 0.52 (21162 hom., cov: 31)
• Consequence: ENSG00000305582 ENST00000811769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.19
• Publications: 58 publications found

Genes affected

ENSG00000305582 (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 (AFR) allele frequency at 95% confidence interval = 0.617 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
ENSG00000305582	ENST00000811769.1	n.66-5447G>A		intron_variant	Intron 1 of 2
ENSG00000305582	ENST00000811770.1	n.122-5447G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79105 AN: 151864 Hom.: 21138 Cov.: 31

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.521 AC: 79151 AN: 151982 Hom.: 21162 Cov.: 31 AF XY: 0.515 AC XY: 38294 AN XY: 74294

African (AFR) AF: 0.624 AC: 25847 AN: 41434

American (AMR) AF: 0.517 AC: 7907 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1993 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1694 AN: 5156

South Asian (SAS) AF: 0.492 AC: 2364 AN: 4800

European-Finnish (FIN) AF: 0.400 AC: 4214 AN: 10548

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33153 AN: 67968

Other (OTH) AF: 0.546 AC: 1156 AN: 2116

Alfa AF: 0.498 Hom.: 86438

Bravo AF: 0.533

Asia WGS AF: 0.394 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.14
DANN	Benign	0.73
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs11676348; hg19: chr2-219010146;