rs10788819

Positions:

• chr1-151922617-C-T

Variant summary

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

The XR_007066624.1(LOC124904421):​n.244-65G>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 0.231 in 151,806 control chromosomes in the GnomAD database, including 4,414 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 0.23 (4414 hom., cov: 32)
• Consequence: LOC124904421 XR_007066624.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

Genes affected

LOC124904421 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904421	XR_007066624.1	n.244-65G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35004 AN: 151688 Hom.: 4416 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.231 AC: 35009 AN: 151806 Hom.: 4414 Cov.: 32 AF XY: 0.233 AC XY: 17288 AN XY: 74208

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.268

Alfa AF: 0.233 Hom.: 9850

Bravo AF: 0.244

Asia WGS AF: 0.296 AC: 1027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10788819; hg19: chr1-151895093;