rs7658334

Variant names:

• chr4-38726455-A-G
• rs7658334
• ENST00000799921.1:n.231+4573A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-38726455-A-G
• chr4-38726455-A-T

Variant summary

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

The ENST00000799921.1(ENSG00000304123):​n.231+4573A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,036 control chromosomes in the GnomAD database, including 27,034 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 0.57 (27034 hom., cov: 31)
• Consequence: ENSG00000304123 ENST00000799921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 5 publications found

Genes affected

ENSG00000304123 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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
ENSG00000304123	ENST00000799921.1	n.231+4573A>G		intron_variant	Intron 2 of 2
ENSG00000304123	ENST00000799922.1	n.174+4573A>G		intron_variant	Intron 2 of 2
ENSG00000304123	ENST00000799923.1	n.152-1383A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85841 AN: 151916 Hom.: 26998 Cov.: 31

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.565 AC: 85935 AN: 152036 Hom.: 27034 Cov.: 31 AF XY: 0.573 AC XY: 42570 AN XY: 74300

African (AFR) AF: 0.750 AC: 31112 AN: 41458

American (AMR) AF: 0.669 AC: 10224 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2137 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5144 AN: 5174

South Asian (SAS) AF: 0.837 AC: 4034 AN: 4818

European-Finnish (FIN) AF: 0.335 AC: 3532 AN: 10546

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27785 AN: 67962

Other (OTH) AF: 0.597 AC: 1262 AN: 2114

Alfa AF: 0.474 Hom.: 78643

Bravo AF: 0.595

Asia WGS AF: 0.887 AC: 3086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.3
DANN	Benign	0.70
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs7658334; hg19: chr4-38728076;