rs12446238

Variant names:

• chr16-62041234-G-A
• rs12446238
• ENST00000798664.1:n.245+4707G>A

Variant summary

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

The ENST00000798664.1(ENSG00000303989):​n.245+4707G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,984 control chromosomes in the GnomAD database, including 21,436 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 0.51 (21436 hom., cov: 32)
• Consequence: ENSG00000303989 ENST00000798664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434
• Publications: 4 publications found

Genes affected

ENSG00000303989 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 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
ENSG00000303989	ENST00000798664.1	n.245+4707G>A		intron_variant	Intron 1 of 3
ENSG00000303989	ENST00000798665.1	n.184+4457G>A		intron_variant	Intron 1 of 3
ENSG00000303989	ENST00000798666.1	n.288+3891G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78081 AN: 151864 Hom.: 21412 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.514 AC: 78140 AN: 151984 Hom.: 21436 Cov.: 32 AF XY: 0.509 AC XY: 37783 AN XY: 74288

African (AFR) AF: 0.711 AC: 29511 AN: 41480

American (AMR) AF: 0.438 AC: 6690 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1985 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1540 AN: 5150

South Asian (SAS) AF: 0.386 AC: 1856 AN: 4812

European-Finnish (FIN) AF: 0.458 AC: 4823 AN: 10524

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30160 AN: 67964

Other (OTH) AF: 0.493 AC: 1042 AN: 2112

Alfa AF: 0.470 Hom.: 9433

Bravo AF: 0.523

Asia WGS AF: 0.378 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.25
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs12446238; hg19: chr16-62075138;