rs601746

chr10-95182526-T-C

Variant summary

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

The XR_007062253.1(LOC107984257):n.348-9339A>G 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 0.16 in 152,236 control chromosomes in the GnomAD database, including 2,144 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 0.16 (2144 hom., cov: 33)
• Consequence: LOC107984257 XR_007062253.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

Genes affected

LOC107984257 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984257	XR_007062253.1	n.348-9339A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24338 AN: 152118 Hom.: 2143 Cov.: 33

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0805

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.160 AC: 24351 AN: 152236 Hom.: 2144 Cov.: 33 AF XY: 0.158 AC XY: 11797 AN XY: 74436

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0805

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.200

Alfa AF: 0.195 Hom.: 2146

Bravo AF: 0.162

Asia WGS AF: 0.0460 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.56
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: rs601746; hg19: chr10-96942283;