rs7009708

Positions:

• chr8-22695176-G-C
• chr8-22695176-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001745832.2(LOC105379321):​n.320G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,022 control chromosomes in the GnomAD database, including 10,322 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 0.36 (10322 hom., cov: 33)
• Consequence: LOC105379321 XR_001745832.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

Genes affected

LOC105379321 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379321	XR_001745832.2	n.320G>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000523627.1	n.164+4863G>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55066 AN: 151906 Hom.: 10299 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.363 AC: 55131 AN: 152022 Hom.: 10322 Cov.: 33 AF XY: 0.363 AC XY: 26986 AN XY: 74316

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.363

Alfa AF: 0.270 Hom.: 743

Bravo AF: 0.360

Asia WGS AF: 0.450 AC: 1559 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	13
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7009708; hg19: chr8-22552689; COSMIC: COSV57833476;