rs1107946

Variant names:

• chr17-50203629-A-C
• rs1107946
• ENST00000509943.2:n.59+3695A>C

Your query was ambiguous. Multiple possible variants found:

• chr17-50203629-A-C
• chr17-50203629-A-G

Variant summary

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

The ENST00000509943.2(ENSG00000249406):​n.59+3695A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,072 control chromosomes in the GnomAD database, including 48,695 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 (48695 hom., cov: 31)
• Consequence: ENSG00000249406 ENST00000509943.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.591

Genes affected

ENSG00000249406 (HGNC:52795): (long intergenic non-protein coding RNA 1969)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249406	ENST00000509943.2	n.59+3695A>C		intron_variant	Intron 1 of 6	3

Frequencies

GnomAD3 genomes AF: 0.796 AC: 121002 AN: 151956 Hom.: 48667 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.796 AC: 121084 AN: 152072 Hom.: 48695 Cov.: 31 AF XY: 0.793 AC XY: 58955 AN XY: 74344

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.802

Alfa AF: 0.830 Hom.: 7643

Bravo AF: 0.783

Asia WGS AF: 0.703 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1107946; hg19: chr17-48280990;