rs2413808

Positions:

• chr15-46417110-G-A
• chr15-46417110-G-C

Variant summary

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

The ENST00000686120.1(ENSG00000287704):​n.56+6757G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,146 control chromosomes in the GnomAD database, including 70,483 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 0.96 (70483 hom., cov: 30)
• Consequence: ENST00000686120.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000686120.1	n.56+6757G>A		intron_variant, non_coding_transcript_variant
	ENST00000661853.1	n.45+6757G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146192 AN: 152028 Hom.: 70433 Cov.: 30

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.985

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.974

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

GnomAD4 genome AF: 0.962 AC: 146301 AN: 152146 Hom.: 70483 Cov.: 30 AF XY: 0.962 AC XY: 71571 AN XY: 74394

Gnomad4 AFR AF: 0.893

Gnomad4 AMR AF: 0.985

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.989

Gnomad4 FIN AF: 0.974

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.974

Alfa AF: 0.986 Hom.: 86401

Bravo AF: 0.959

Asia WGS AF: 0.988 AC: 3436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2413808; hg19: chr15-46709308;