rs815583

Variant names:

• chr6-285695-G-A
• rs815583
• ENST00000665870.1:n.3232C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-285695-G-A
• chr6-285695-G-C
• chr6-285695-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665870.1(ENSG00000287265):​n.3232C>T 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 0.78 in 152,146 control chromosomes in the GnomAD database, including 43,201 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 0.78 (43201 hom., cov: 51)
• Consequence: ENSG00000287265 ENST00000665870.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

ENSG00000287265 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 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
ENSG00000287265	ENST00000665870.1	n.3232C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118555 AN: 152028 Hom.: 43159 Cov.: 51

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.780 AC: 118657 AN: 152146 Hom.: 43201 Cov.: 51 AF XY: 0.782 AC XY: 58198 AN XY: 74382

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.787

Alfa AF: 0.800 Hom.: 6737

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.61
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs815583; hg19: chr6-285695;