rs10911707

Positions:

• chr1-185335727-G-A

Variant summary

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

The XR_007066771.1(CBSLR):​n.826+17450G>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 0.524 in 151,988 control chromosomes in the GnomAD database, including 23,158 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 0.52 (23158 hom., cov: 32)
• Consequence: CBSLR XR_007066771.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.97

Genes affected

CBSLR (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CBSLR	XR_007066771.1	n.826+17450G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79589 AN: 151870 Hom.: 23120 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.524 AC: 79678 AN: 151988 Hom.: 23158 Cov.: 32 AF XY: 0.519 AC XY: 38555 AN XY: 74298

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.467

Alfa AF: 0.451 Hom.: 16241

Bravo AF: 0.529

Asia WGS AF: 0.416 AC: 1448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0020
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10911707; hg19: chr1-185304859;