rs2934193

chr15-47967522-T-C

Variant summary

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

The ENST00000657831.1(ENSG00000287439):n.409-6897A>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 0.57 in 151,996 control chromosomes in the GnomAD database, including 31,038 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 0.57 (31038 hom., cov: 31)
• Consequence: ENST00000657831.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

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 (NFE) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900354	XR_001751516.3	n.143-25187T>C		intron_variant, non_coding_transcript_variant
LOC102724553	XR_001751520.2	n.481-6897A>G		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751517.2	n.143-25187T>C		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751518.3	n.83-25187T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657831.1	n.409-6897A>G		intron_variant, non_coding_transcript_variant
	ENST00000662551.1	n.189-25187T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86729 AN: 151878 Hom.: 31050 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.570 AC: 86709 AN: 151996 Hom.: 31038 Cov.: 31 AF XY: 0.571 AC XY: 42376 AN XY: 74268

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.600

Alfa AF: 0.741 Hom.: 19752

Bravo AF: 0.530

Asia WGS AF: 0.351 AC: 1223 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	1.4
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2934193; hg19: chr15-48259719;