rs4741651

Positions:

• chr9-2194030-C-T

Variant summary

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

The XR_007061395.1(LOC107987043):​n.302-13008G>A 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 0.235 in 152,104 control chromosomes in the GnomAD database, including 5,265 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 0.23 (5265 hom., cov: 33)
• Consequence: LOC107987043 XR_007061395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

Genes affected

LOC107987043 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987043	XR_007061395.1	n.302-13008G>A		intron_variant, non_coding_transcript_variant
LOC107987043	XR_001746600.2	n.298-13008G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35630 AN: 151986 Hom.: 5245 Cov.: 33

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.235 AC: 35693 AN: 152104 Hom.: 5265 Cov.: 33 AF XY: 0.234 AC XY: 17428 AN XY: 74358

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.226

Alfa AF: 0.186 Hom.: 1373

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4741651; hg19: chr9-2194030; COSMIC: COSV56648853;