9-2210993-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.301+19588G>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 0.281 in 152,020 control chromosomes in the GnomAD database, including 6,670 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 0.28 (6670 hom., cov: 32)
• Consequence: LOC107987043 XR_007061395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

Genes affected

LOC107987043 (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 (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987043	XR_007061395.1	n.301+19588G>A		intron_variant, non_coding_transcript_variant
LOC107987043	XR_001746600.2	n.297+19588G>A		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: 42699 AN: 151902 Hom.: 6659 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0800

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.281 AC: 42733 AN: 152020 Hom.: 6670 Cov.: 32 AF XY: 0.277 AC XY: 20585 AN XY: 74322

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.0802

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.284

Alfa AF: 0.243 Hom.: 4598

Bravo AF: 0.297

Asia WGS AF: 0.198 AC: 692 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.4
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7863990; hg19: chr9-2210993; COSMIC: COSV69442477;