rs4641644

Variant names:

• chr14-43334278-C-A
• rs4641644
• ENST00000807481.1:n.518-28G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-43334278-C-A
• chr14-43334278-C-G

Variant summary

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

The ENST00000807481.1(ENSG00000304974):​n.518-28G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,152 control chromosomes in the GnomAD database, including 1,781 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 0.13 (1781 hom., cov: 33)
• Consequence: ENSG00000304974 ENST00000807481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 1 publications found

Genes affected

ENSG00000304974 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807481.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304974	ENST00000807481.1		n.518-28G>T		intron	N/A
	ENSG00000304974	ENST00000807482.1		n.627-28G>T		intron	N/A
	ENSG00000304974	ENST00000807483.1		n.363-28G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20351 AN: 152034 Hom.: 1768 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.0718

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.134 AC: 20400 AN: 152152 Hom.: 1781 Cov.: 33 AF XY: 0.139 AC XY: 10360 AN XY: 74376

African (AFR) AF: 0.187 AC: 7764 AN: 41500

American (AMR) AF: 0.224 AC: 3422 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3470

East Asian (EAS) AF: 0.341 AC: 1757 AN: 5156

South Asian (SAS) AF: 0.114 AC: 548 AN: 4824

European-Finnish (FIN) AF: 0.103 AC: 1087 AN: 10604

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.0718 AC: 4881 AN: 67998

Other (OTH) AF: 0.134 AC: 282 AN: 2110

Alfa AF: 0.0960 Hom.: 505

Bravo AF: 0.149

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.74
PhyloP100		-0.24

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4641644;

hg19: chr14-43803481;