rs10917851

chr1-163800343-A-G

Variant summary

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

The XR_007066704.1(LOC124904447):n.162-24641A>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 0.136 in 151,782 control chromosomes in the GnomAD database, including 3,347 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 0.14 (3347 hom., cov: 32)
• Consequence: LOC124904447 XR_007066704.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.806

Genes affected

LOC124904447 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904447	XR_007066704.1	n.162-24641A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20523 AN: 151664 Hom.: 3326 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0272

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.136 AC: 20595 AN: 151782 Hom.: 3347 Cov.: 32 AF XY: 0.133 AC XY: 9875 AN XY: 74166

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.0765

Gnomad4 ASJ AF: 0.0317

Gnomad4 EAS AF: 0.0597

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.0272

Gnomad4 NFE AF: 0.0309

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0776 Hom.: 345

Bravo AF: 0.150

Asia WGS AF: 0.0630 AC: 217 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.8
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10917851; hg19: chr1-163769580;