rs16960516

Positions:

• chr15-48037345-A-G

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.252-11445A>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 0.0562 in 152,292 control chromosomes in the GnomAD database, including 348 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 0.056 (348 hom., cov: 32)
• Consequence: ENST00000662551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900354	XR_001751516.3	n.206-11445A>G		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751518.3	n.146-11445A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662551.1	n.252-11445A>G		intron_variant, non_coding_transcript_variant
	ENST00000560900.1	n.259-11445A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000665188.1	n.221-11492A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0563 AC: 8566 AN: 152174 Hom.: 350 Cov.: 32

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0348

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.00539

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0562 AC: 8562 AN: 152292 Hom.: 348 Cov.: 32 AF XY: 0.0588 AC XY: 4381 AN XY: 74460

Gnomad4 AFR AF: 0.0136

Gnomad4 AMR AF: 0.0348

Gnomad4 ASJ AF: 0.0992

Gnomad4 EAS AF: 0.00540

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0745

Gnomad4 OTH AF: 0.0421

Alfa AF: 0.0630 Hom.: 76

Bravo AF: 0.0469

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.99
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16960516; hg19: chr15-48329542;