rs7939734

Variant names:

• chr11-70208839-T-A
• rs7939734
• ENST00000808877.1:n.484-185A>T

Your query was ambiguous. Multiple possible variants found:

• chr11-70208839-T-A
• chr11-70208839-T-C

Variant summary

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

The ENST00000808877.1(ENSG00000254721):​n.484-185A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,922 control chromosomes in the GnomAD database, including 24,939 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 (24939 hom., cov: 32)
• Consequence: ENSG00000254721 ENST00000808877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606
• Publications: 7 publications found

Genes affected

ENSG00000254721 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808877.1. 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
	ENSG00000254721	ENST00000808877.1		n.484-185A>T		intron	N/A
	ENSG00000254721	ENST00000808878.1		n.493-262A>T		intron	N/A
	ENSG00000254721	ENST00000808879.1		n.485-185A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86470 AN: 151806 Hom.: 24896 Cov.: 32

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.570 AC: 86567 AN: 151922 Hom.: 24939 Cov.: 32 AF XY: 0.568 AC XY: 42147 AN XY: 74232

African (AFR) AF: 0.611 AC: 25301 AN: 41428

American (AMR) AF: 0.483 AC: 7372 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2199 AN: 3470

East Asian (EAS) AF: 0.666 AC: 3425 AN: 5144

South Asian (SAS) AF: 0.433 AC: 2080 AN: 4802

European-Finnish (FIN) AF: 0.584 AC: 6173 AN: 10570

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38365 AN: 67926

Other (OTH) AF: 0.558 AC: 1177 AN: 2108

Alfa AF: 0.566 Hom.: 3036

Bravo AF: 0.565

Asia WGS AF: 0.563 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.46
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs7939734; hg19: chr11-70054945;