rs1939875

Positions:

• chr11-95689703-A-G
• chr11-95689703-A-T

Variant summary

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

The ENST00000648353.1(ENSG00000285842):​n.526-55016A>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 0.742 in 152,004 control chromosomes in the GnomAD database, including 42,029 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 0.74 (42029 hom., cov: 31)
• Consequence: ENST00000648353.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648353.1	n.526-55016A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112677 AN: 151886 Hom.: 41977 Cov.: 31

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.742 AC: 112780 AN: 152004 Hom.: 42029 Cov.: 31 AF XY: 0.738 AC XY: 54855 AN XY: 74294

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.743

Alfa AF: 0.722 Hom.: 82642

Bravo AF: 0.749

Asia WGS AF: 0.740 AC: 2574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
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: rs1939875; hg19: chr11-95422867;