chr1-185335727-G-A

Variant names:

• chr1-185335727-G-A
• rs10911707
• ENST00000809379.1:n.168+17450G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000809379.1(ENSG00000273004):​n.168+17450G>A variant causes a intron 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: ENSG00000273004 ENST00000809379.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.97
• Publications: 3 publications found

Genes affected

ENSG00000273004 (HGNC:):

CBSLR (HGNC:55459): (CBS mRNA stabilizing lncRNA)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809379.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000273004	ENST00000809379.1		n.168+17450G>A		intron	N/A
	ENSG00000273004	ENST00000809380.1		n.186+17450G>A		intron	N/A

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

African (AFR) AF: 0.789 AC: 32684 AN: 41436

American (AMR) AF: 0.365 AC: 5571 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1309 AN: 3466

East Asian (EAS) AF: 0.330 AC: 1705 AN: 5162

South Asian (SAS) AF: 0.521 AC: 2510 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4388 AN: 10562

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30014 AN: 67960

Other (OTH) AF: 0.467 AC: 987 AN: 2112

Alfa AF: 0.462 Hom.: 22537

Bravo AF: 0.529

Asia WGS AF: 0.416 AC: 1448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0020
DANN	Benign	0.39
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs10911707; hg19: chr1-185304859;