rs16960341

chr15-47917521-C-Achr15-47917521-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000662551.1(ENSG00000259754):n.189-75188C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 31)
• Consequence: ENST00000662551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900354	XR_001751516.3	n.142+33017C>A		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751517.2	n.142+33017C>A		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751518.3	n.82+2159C>A		intron_variant, non_coding_transcript_variant
LOC124900354	XR_007064618.1	n.143-31835C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662551.1	n.189-75188C>A		intron_variant, non_coding_transcript_variant
	ENST00000560900.1	n.195+33017C>A		intron_variant, non_coding_transcript_variant		4
	ENST00000664705.1	n.189-75188C>A		intron_variant, non_coding_transcript_variant
	ENST00000665188.1	n.69-75188C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.56
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16960341; hg19: chr15-48209718;