rs621942

Variant names:

• chr11-86072696-C-A
• rs621942
• ENST00000845444.1:n.*195C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-86072696-C-A
• chr11-86072696-C-G
• chr11-86072696-C-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000845444.1(ENSG00000309910):​n.*195C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,874 control chromosomes in the GnomAD database, including 5,425 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 0.26 (5425 hom., cov: 32)
• Consequence: ENSG00000309910 ENST00000845444.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 11 publications found

Genes affected

ENSG00000309910 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000845444.1. 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
	ENSG00000309910	ENST00000845444.1		n.*195C>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39550 AN: 151754 Hom.: 5425 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.261 AC: 39572 AN: 151874 Hom.: 5425 Cov.: 32 AF XY: 0.258 AC XY: 19117 AN XY: 74226

African (AFR) AF: 0.331 AC: 13694 AN: 41392

American (AMR) AF: 0.271 AC: 4131 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 865 AN: 3462

East Asian (EAS) AF: 0.112 AC: 580 AN: 5166

South Asian (SAS) AF: 0.282 AC: 1355 AN: 4810

European-Finnish (FIN) AF: 0.149 AC: 1574 AN: 10534

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16417 AN: 67932

Other (OTH) AF: 0.257 AC: 542 AN: 2106

Alfa AF: 0.247 Hom.: 19701

Bravo AF: 0.270

Asia WGS AF: 0.182 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	10
DANN	Benign	0.75
PhyloP100		0.26

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: rs621942;

hg19: chr11-85783738;