rs4904947

Variant names:

• chr14-92505818-C-T
• rs4904947
• ENST00000832990.1:n.161-1507G>A

Variant summary

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

The ENST00000832990.1(ENSG00000308283):​n.161-1507G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,132 control chromosomes in the GnomAD database, including 3,829 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 0.20 (3829 hom., cov: 32)
• Consequence: ENSG00000308283 ENST00000832990.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566
• Publications: 13 publications found

Genes affected

ENSG00000308283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.306 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
ENSG00000308283	ENST00000832990.1	n.161-1507G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30901 AN: 152014 Hom.: 3832 Cov.: 32

Gnomad AFR AF: 0.0650

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.203 AC: 30908 AN: 152132 Hom.: 3829 Cov.: 32 AF XY: 0.209 AC XY: 15540 AN XY: 74342

African (AFR) AF: 0.0649 AC: 2695 AN: 41538

American (AMR) AF: 0.314 AC: 4790 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1253 AN: 5168

South Asian (SAS) AF: 0.200 AC: 966 AN: 4818

European-Finnish (FIN) AF: 0.288 AC: 3032 AN: 10542

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16462 AN: 68000

Other (OTH) AF: 0.225 AC: 476 AN: 2114

Alfa AF: 0.231 Hom.: 13482

Bravo AF: 0.199

Asia WGS AF: 0.205 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs4904947; hg19: chr14-92972162;