rs12644436

Variant names:

• chr4-87884056-A-G
• rs12644436
• ENST00000829020.1:n.285+8197T>C

Variant summary

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

The ENST00000829020.1(ENSG00000307815):​n.285+8197T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,844 control chromosomes in the GnomAD database, including 24,578 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 0.57 (24578 hom., cov: 30)
• Consequence: ENSG00000307815 ENST00000829020.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 13 publications found

Genes affected

ENSG00000307815 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 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
ENSG00000307815	ENST00000829020.1	n.285+8197T>C		intron_variant	Intron 3 of 5
ENSG00000307815	ENST00000829021.1	n.340+8197T>C		intron_variant	Intron 3 of 4
ENSG00000307815	ENST00000829022.1	n.335+8197T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86193 AN: 151726 Hom.: 24556 Cov.: 30

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.568 AC: 86263 AN: 151844 Hom.: 24578 Cov.: 30 AF XY: 0.567 AC XY: 42061 AN XY: 74186

African (AFR) AF: 0.608 AC: 25158 AN: 41390

American (AMR) AF: 0.541 AC: 8268 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1703 AN: 3468

East Asian (EAS) AF: 0.570 AC: 2928 AN: 5136

South Asian (SAS) AF: 0.501 AC: 2418 AN: 4824

European-Finnish (FIN) AF: 0.593 AC: 6239 AN: 10526

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37745 AN: 67918

Other (OTH) AF: 0.598 AC: 1259 AN: 2106

Alfa AF: 0.557 Hom.: 96004

Bravo AF: 0.564

Asia WGS AF: 0.566 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.7
DANN	Benign	0.54
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs12644436; hg19: chr4-88805208;