rs3037354

chr7-24283306-CTG-Cchr7-24283306-CTG-CTGTG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XR_001745132.2(LOC107986777):n.209+36049_209+36050del 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 0.281 in 152,044 control chromosomes in the GnomAD database, including 6,174 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6174 hom., cov: 19)
• Consequence: LOC107986777 XR_001745132.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796

Genes affected

LOC107986777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.209+36049_209+36050del		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42663 AN: 151926 Hom.: 6166 Cov.: 19

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.281 AC: 42692 AN: 152044 Hom.: 6174 Cov.: 19 AF XY: 0.280 AC XY: 20794 AN XY: 74336

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.285

Alfa AF: 0.268 Hom.: 710

Bravo AF: 0.281

Asia WGS AF: 0.310 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3037354; hg19: chr7-24322925;