rs6497031

Variant names:

• chr15-93170437-G-A
• rs6497031
• ENST00000711606.1:n.513-6G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-93170437-G-A
• chr15-93170437-G-C

Variant summary

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

The ENST00000711606.1(ENSG00000257060):​n.513-6G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,090 control chromosomes in the GnomAD database, including 2,858 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 (2858 hom., cov: 32)
• Consequence: ENSG00000257060 ENST00000711606.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 3 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000711606.1. 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
	ENSG00000257060	ENST00000711606.1		n.513-6G>A		splice_region intron	N/A
	ENSG00000257060	ENST00000791023.1		n.204-6G>A		splice_region intron	N/A
	ENSG00000257060	ENST00000791051.1		n.417-6G>A		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28734 AN: 151972 Hom.: 2856 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.189 AC: 28765 AN: 152090 Hom.: 2858 Cov.: 32 AF XY: 0.189 AC XY: 14078 AN XY: 74338

African (AFR) AF: 0.259 AC: 10745 AN: 41458

American (AMR) AF: 0.204 AC: 3114 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3468

East Asian (EAS) AF: 0.139 AC: 719 AN: 5166

South Asian (SAS) AF: 0.176 AC: 849 AN: 4822

European-Finnish (FIN) AF: 0.153 AC: 1621 AN: 10576

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10736 AN: 68000

Other (OTH) AF: 0.173 AC: 366 AN: 2112

Alfa AF: 0.154 Hom.: 1598

Bravo AF: 0.195

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.63
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs6497031; hg19: chr15-93713666;