rs932316

Variant names:

• chr6-25640972-T-C
• rs932316
• ENST00000662203.1:n.-41A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-25640972-T-C
• chr6-25640972-T-G

Variant summary

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

The ENST00000662203.1(ENSG00000286933):​n.-41A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,164 control chromosomes in the GnomAD database, including 2,734 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 0.19 (2734 hom., cov: 32)
• Consequence: ENSG00000286933 ENST00000662203.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 18 publications found

Genes affected

ENSG00000286933 (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 (AFR) allele frequency at 95% confidence interval = 0.199 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
ENSG00000286933	ENST00000662203.1	n.-41A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28551 AN: 152046 Hom.: 2720 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.188 AC: 28594 AN: 152164 Hom.: 2734 Cov.: 32 AF XY: 0.187 AC XY: 13900 AN XY: 74412

African (AFR) AF: 0.203 AC: 8418 AN: 41528

American (AMR) AF: 0.171 AC: 2612 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3470

East Asian (EAS) AF: 0.151 AC: 780 AN: 5166

South Asian (SAS) AF: 0.190 AC: 915 AN: 4826

European-Finnish (FIN) AF: 0.169 AC: 1785 AN: 10584

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12988 AN: 67980

Other (OTH) AF: 0.211 AC: 446 AN: 2112

Alfa AF: 0.182 Hom.: 7002

Bravo AF: 0.190

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs932316; hg19: chr6-25641200;