rs1107946

Positions:

• 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, non coding transcript 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: ENST00000509943.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.591

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000509943.2	n.59+3695A>C		intron_variant, non_coding_transcript_variant		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;