ENST00000820764.1:n.457-12175C>A

Variant names:

• chr7-131603231-C-A
• rs12534221
• ENST00000820764.1:n.457-12175C>A

Variant summary

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

The ENST00000820764.1(ENSG00000306749):​n.457-12175C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,136 control chromosomes in the GnomAD database, including 1,694 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 0.13 (1694 hom., cov: 32)
• Consequence: ENSG00000306749 ENST00000820764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783
• Publications: 12 publications found

Genes affected

ENSG00000306749 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 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
ENSG00000306749	ENST00000820764.1	n.457-12175C>A		intron_variant	Intron 3 of 3
ENSG00000306749	ENST00000820765.1	n.435-12175C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20375 AN: 152018 Hom.: 1697 Cov.: 32

Gnomad AFR AF: 0.0509

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.134 AC: 20372 AN: 152136 Hom.: 1694 Cov.: 32 AF XY: 0.137 AC XY: 10223 AN XY: 74354

African (AFR) AF: 0.0508 AC: 2109 AN: 41534

American (AMR) AF: 0.161 AC: 2461 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1512 AN: 5136

South Asian (SAS) AF: 0.162 AC: 781 AN: 4814

European-Finnish (FIN) AF: 0.206 AC: 2182 AN: 10570

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10384 AN: 68004

Other (OTH) AF: 0.149 AC: 315 AN: 2112

Alfa AF: 0.149 Hom.: 6176

Bravo AF: 0.129

Asia WGS AF: 0.214 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.0
DANN	Benign	0.58
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs12534221; hg19: chr7-131287990;