rs7597224

Positions:

• chr2-18784356-C-A

Variant summary

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

The XR_007086234.1(LOC105373456):​n.973+96028C>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 0.336 in 152,022 control chromosomes in the GnomAD database, including 9,086 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 0.34 (9086 hom., cov: 32)
• Consequence: LOC105373456 XR_007086234.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

LOC105373456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373456	XR_007086234.1	n.973+96028C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50997 AN: 151904 Hom.: 9082 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.336 AC: 51008 AN: 152022 Hom.: 9086 Cov.: 32 AF XY: 0.336 AC XY: 24974 AN XY: 74298

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.341

Alfa AF: 0.375 Hom.: 5083

Bravo AF: 0.326

Asia WGS AF: 0.303 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7597224; hg19: chr2-18965622;