rs6884962

Variant names:

• chr5-173255379-G-A
• rs6884962
• ENST00000837826.1:n.205-7621G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-173255379-G-A
• chr5-173255379-G-C

Variant summary

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

The ENST00000837826.1(ENSG00000309012):​n.205-7621G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,248 control chromosomes in the GnomAD database, including 13,227 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 0.41 (13227 hom., cov: 33)
• Consequence: ENSG00000309012 ENST00000837826.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 4 publications found

Genes affected

ENSG00000309012 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 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
ENSG00000309012	ENST00000837826.1	n.205-7621G>A		intron_variant	Intron 1 of 4
ENSG00000309012	ENST00000837827.1	n.180-7621G>A		intron_variant	Intron 1 of 3
ENSG00000309012	ENST00000837828.1	n.156-7621G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62020 AN: 151136 Hom.: 13212 Cov.: 33

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.410 AC: 62075 AN: 151248 Hom.: 13227 Cov.: 33 AF XY: 0.417 AC XY: 30859 AN XY: 73916

African (AFR) AF: 0.445 AC: 18110 AN: 40742

American (AMR) AF: 0.523 AC: 7977 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3464

East Asian (EAS) AF: 0.689 AC: 3559 AN: 5166

South Asian (SAS) AF: 0.430 AC: 2070 AN: 4816

European-Finnish (FIN) AF: 0.424 AC: 4475 AN: 10550

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.346 AC: 23531 AN: 67960

Other (OTH) AF: 0.414 AC: 870 AN: 2100

Alfa AF: 0.372 Hom.: 17386

Bravo AF: 0.421

Asia WGS AF: 0.508 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.38
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs6884962; hg19: chr5-172682382;