rs4740995

Variant names:

• chr9-1004958-A-G
• rs4740995
• ENST00000823816.1:n.411+1604A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-1004958-A-G
• chr9-1004958-A-T

Variant summary

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

The ENST00000823816.1(ENSG00000307091):​n.411+1604A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,206 control chromosomes in the GnomAD database, including 50,162 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 0.81 (50162 hom., cov: 33)
• Consequence: ENSG00000307091 ENST00000823816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• Publications: 2 publications found

Genes affected

ENSG00000307091 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000823816.1. 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
	ENSG00000307091	ENST00000823816.1		n.411+1604A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122575 AN: 152088 Hom.: 50092 Cov.: 33

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.806 AC: 122709 AN: 152206 Hom.: 50162 Cov.: 33 AF XY: 0.810 AC XY: 60266 AN XY: 74398

African (AFR) AF: 0.929 AC: 38573 AN: 41542

American (AMR) AF: 0.820 AC: 12541 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2528 AN: 3472

East Asian (EAS) AF: 0.990 AC: 5134 AN: 5186

South Asian (SAS) AF: 0.716 AC: 3447 AN: 4816

European-Finnish (FIN) AF: 0.797 AC: 8446 AN: 10598

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49386 AN: 67980

Other (OTH) AF: 0.782 AC: 1653 AN: 2114

Alfa AF: 0.781 Hom.: 32474

Bravo AF: 0.817

Asia WGS AF: 0.879 AC: 3053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.56
PhyloP100		0.38

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: rs4740995;

hg19: chr9-1004958;