rs12646889

Variant names:

• chr4-74347559-G-A
• rs12646889
• ENST00000805841.1:n.192-17255C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-74347559-G-A
• chr4-74347559-G-T

Variant summary

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

The ENST00000805841.1(ENSG00000304732):​n.192-17255C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,906 control chromosomes in the GnomAD database, including 9,540 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 0.34 (9540 hom., cov: 32)
• Consequence: ENSG00000304732 ENST00000805841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 4 publications found

Genes affected

ENSG00000304732 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377276	NR_188415.1	n.192-17255C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304732	ENST00000805841.1	n.192-17255C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51910 AN: 151788 Hom.: 9517 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.342 AC: 51992 AN: 151906 Hom.: 9540 Cov.: 32 AF XY: 0.348 AC XY: 25811 AN XY: 74222

African (AFR) AF: 0.443 AC: 18359 AN: 41442

American (AMR) AF: 0.402 AC: 6128 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3472

East Asian (EAS) AF: 0.467 AC: 2411 AN: 5164

South Asian (SAS) AF: 0.453 AC: 2181 AN: 4818

European-Finnish (FIN) AF: 0.295 AC: 3109 AN: 10544

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17903 AN: 67916

Other (OTH) AF: 0.314 AC: 662 AN: 2110

Alfa AF: 0.326 Hom.: 1492

Bravo AF: 0.354

Asia WGS AF: 0.474 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.20
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12646889; hg19: chr4-75213276;