chr12-18811632-A-G

Variant names:

• chr12-18811632-A-G
• rs7961337
• ENST00000838343.1:n.200-4542A>G

Variant summary

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

The ENST00000838343.1(ENSG00000309085):​n.200-4542A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,210 control chromosomes in the GnomAD database, including 1,922 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 0.12 (1922 hom., cov: 32)
• Consequence: ENSG00000309085 ENST00000838343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416
• Publications: 5 publications found

Genes affected

ENSG00000309085 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724227	XR_001749032.2	n.2745-1658A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309085	ENST00000838343.1	n.200-4542A>G		intron_variant	Intron 3 of 3
ENSG00000309085	ENST00000838344.1	n.183-1658A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18119 AN: 152092 Hom.: 1909 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.0449

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0391

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.119 AC: 18158 AN: 152210 Hom.: 1922 Cov.: 32 AF XY: 0.123 AC XY: 9152 AN XY: 74424

African (AFR) AF: 0.214 AC: 8863 AN: 41498

American (AMR) AF: 0.227 AC: 3477 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0449 AC: 156 AN: 3472

East Asian (EAS) AF: 0.389 AC: 2009 AN: 5168

South Asian (SAS) AF: 0.119 AC: 574 AN: 4826

European-Finnish (FIN) AF: 0.0391 AC: 415 AN: 10614

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0349 AC: 2375 AN: 68020

Other (OTH) AF: 0.114 AC: 241 AN: 2114

Alfa AF: 0.0688 Hom.: 3224

Bravo AF: 0.141

Asia WGS AF: 0.251 AC: 872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.36
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs7961337; hg19: chr12-18964566;