rs6867913

Variant names:

• chr5-142066415-G-A
• rs6867913
• ENST00000836955.1:n.189G>A

Variant summary

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

The ENST00000836955.1(ENSG00000308869):​n.189G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,126 control chromosomes in the GnomAD database, including 3,603 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 0.20 (3603 hom., cov: 31)
• Consequence: ENSG00000308869 ENST00000836955.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60
• Publications: 13 publications found

Genes affected

ENSG00000308869 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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
ENSG00000308869	ENST00000836955.1	n.189G>A		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000308869	ENST00000836956.1	n.227G>A		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000308869	ENST00000836957.1	n.179G>A		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29807 AN: 152008 Hom.: 3591 Cov.: 31

Gnomad AFR AF: 0.0986

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.196 AC: 29829 AN: 152126 Hom.: 3603 Cov.: 31 AF XY: 0.201 AC XY: 14956 AN XY: 74358

African (AFR) AF: 0.0984 AC: 4084 AN: 41522

American (AMR) AF: 0.300 AC: 4582 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3468

East Asian (EAS) AF: 0.504 AC: 2603 AN: 5162

South Asian (SAS) AF: 0.327 AC: 1573 AN: 4814

European-Finnish (FIN) AF: 0.200 AC: 2113 AN: 10582

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13850 AN: 67978

Other (OTH) AF: 0.187 AC: 395 AN: 2110

Alfa AF: 0.207 Hom.: 14104

Bravo AF: 0.200

Asia WGS AF: 0.375 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.58
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs6867913; hg19: chr5-141445980;