rs4741658

Positions:

• chr9-2241994-G-A
• chr9-2241994-G-C
• chr9-2241994-G-T

Variant summary

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

The XR_007061395.1(LOC107987043):​n.193+433C>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 0.247 in 152,094 control chromosomes in the GnomAD database, including 6,533 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 0.25 (6533 hom., cov: 32)
• Consequence: LOC107987043 XR_007061395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

Genes affected

LOC107987043 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987043	XR_007061395.1	n.193+433C>T		intron_variant, non_coding_transcript_variant
LOC107987043	XR_001746600.2	n.189+433C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37531 AN: 151976 Hom.: 6529 Cov.: 32

Gnomad AFR AF: 0.0648

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.247 AC: 37539 AN: 152094 Hom.: 6533 Cov.: 32 AF XY: 0.258 AC XY: 19196 AN XY: 74334

Gnomad4 AFR AF: 0.0646

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.253

Alfa AF: 0.262 Hom.: 7440

Bravo AF: 0.244

Asia WGS AF: 0.523 AC: 1815 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	0.25
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4741658; hg19: chr9-2241994; COSMIC: COSV69442576;