rs4743837

Variant names:

• chr9-91484490-G-A
• rs4743837
• ENST00000730195.1:n.482C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-91484490-G-A
• chr9-91484490-G-T

Variant summary

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

The ENST00000730195.1(ENSG00000295449):​n.482C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,994 control chromosomes in the GnomAD database, including 1,976 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 0.15 (1976 hom., cov: 31)
• Consequence: ENSG00000295449 ENST00000730195.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 5 publications found

Genes affected

ENSG00000295449 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 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
ENSG00000295449	ENST00000730195.1	n.482C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23190 AN: 151876 Hom.: 1977 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.153 AC: 23181 AN: 151994 Hom.: 1976 Cov.: 31 AF XY: 0.150 AC XY: 11142 AN XY: 74272

African (AFR) AF: 0.103 AC: 4251 AN: 41452

American (AMR) AF: 0.132 AC: 2022 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3468

East Asian (EAS) AF: 0.132 AC: 677 AN: 5144

South Asian (SAS) AF: 0.183 AC: 883 AN: 4812

European-Finnish (FIN) AF: 0.145 AC: 1527 AN: 10564

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12458 AN: 67976

Other (OTH) AF: 0.175 AC: 369 AN: 2110

Alfa AF: 0.145 Hom.: 835

Bravo AF: 0.151

Asia WGS AF: 0.152 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs4743837; hg19: chr9-94246772; COSMIC: COSV60378253;