rs2940775

Positions:

• chr4-23347368-C-A
• chr4-23347368-C-G
• chr4-23347368-C-T

Variant summary

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

The XR_925461.2(LOC105374523):​n.266-17925G>T 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 0.795 in 151,872 control chromosomes in the GnomAD database, including 48,173 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 0.79 (48173 hom., cov: 30)
• Consequence: LOC105374523 XR_925461.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

Genes affected

LOC105374523 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374523	XR_925461.2	n.266-17925G>T		intron_variant, non_coding_transcript_variant
LOC105374523	XR_001741614.1	n.227-17925G>T		intron_variant, non_coding_transcript_variant
LOC105374524	XR_007058437.1	n.2932+13842C>A		intron_variant, non_coding_transcript_variant
LOC105374523	XR_925460.2	n.227-17925G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120602 AN: 151754 Hom.: 48126 Cov.: 30

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.795 AC: 120709 AN: 151872 Hom.: 48173 Cov.: 30 AF XY: 0.799 AC XY: 59312 AN XY: 74248

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.823

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.806

Alfa AF: 0.755 Hom.: 8827

Bravo AF: 0.805

Asia WGS AF: 0.911 AC: 3169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2940775; hg19: chr4-23348991;