rs935053

Variant names:

• chr9-21783923-G-A
• rs935053
• ENST00000765951.1:n.155-6921G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-21783923-G-A
• chr9-21783923-G-T

Variant summary

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

The ENST00000765951.1(ENSG00000299739):​n.155-6921G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,034 control chromosomes in the GnomAD database, including 29,740 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 0.61 (29740 hom., cov: 28)
• Consequence: ENSG00000299739 ENST00000765951.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 10 publications found

Genes affected

ENSG00000299739 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765951.1. 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
	ENSG00000299739	ENST00000765951.1		n.155-6921G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.614 AC: 92705 AN: 150926 Hom.: 29675 Cov.: 28

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.615 AC: 92836 AN: 151034 Hom.: 29740 Cov.: 28 AF XY: 0.610 AC XY: 45000 AN XY: 73744

African (AFR) AF: 0.812 AC: 33465 AN: 41196

American (AMR) AF: 0.603 AC: 9149 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1911 AN: 3466

East Asian (EAS) AF: 0.710 AC: 3652 AN: 5144

South Asian (SAS) AF: 0.428 AC: 2049 AN: 4782

European-Finnish (FIN) AF: 0.525 AC: 5363 AN: 10206

Middle Eastern (MID) AF: 0.476 AC: 138 AN: 290

European-Non Finnish (NFE) AF: 0.524 AC: 35506 AN: 67764

Other (OTH) AF: 0.582 AC: 1220 AN: 2098

Alfa AF: 0.589 Hom.: 3330

Bravo AF: 0.636

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.55
PhyloP100		-0.29

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: rs935053;

hg19: chr9-21783922;