15-63104668-A-G

Position:

• chr15-63104668-A-G

Variant summary

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

The ENST00000665500.1(ENSG00000259672):​n.260-417A>G 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 0.78 in 151,954 control chromosomes in the GnomAD database, including 46,572 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 (46572 hom., cov: 30)
• Consequence: ENST00000665500.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.54

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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
	ENST00000665500.1	n.260-417A>G		intron_variant, non_coding_transcript_variant
	ENST00000560238.1	n.112-417A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000648659.1	n.434-417A>G		intron_variant, non_coding_transcript_variant
	ENST00000656894.1	n.3-417A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118394 AN: 151836 Hom.: 46537 Cov.: 30

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.780 AC: 118488 AN: 151954 Hom.: 46572 Cov.: 30 AF XY: 0.781 AC XY: 58042 AN XY: 74282

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.768

Alfa AF: 0.800 Hom.: 53957

Bravo AF: 0.784

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.20
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: rs2652834; hg19: chr15-63396867;