rs815583

Positions:

• 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: ENST00000665870.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665870.1	n.3232C>T		non_coding_transcript_exon_variant	3/3

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;