rs1630535

chr15-60217977-A-Gchr15-60217977-A-T

Variant summary

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

The ENST00000662300.1(ENSG00000287915):n.318T>C 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 0.804 in 152,014 control chromosomes in the GnomAD database, including 49,615 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 0.80 (49615 hom., cov: 30)
• Consequence: ENST00000662300.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370839	XR_932310.3	n.354-34448A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662300.1	n.318T>C		non_coding_transcript_exon_variant	2/3

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122179 AN: 151896 Hom.: 49583 Cov.: 30

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.804 AC: 122267 AN: 152014 Hom.: 49615 Cov.: 30 AF XY: 0.807 AC XY: 59893 AN XY: 74258

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.888

Gnomad4 ASJ AF: 0.906

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.828

Alfa AF: 0.847 Hom.: 71822

Bravo AF: 0.807

Asia WGS AF: 0.832 AC: 2893 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.4
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1630535; hg19: chr15-60510176;