rs1016091

Variant names:

• chr1-34458995-C-T
• rs1016091
• XR_001737964.2:n.936-95G>A

Variant summary

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

The XR_001737964.2(LOC105378641):​n.936-95G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,072 control chromosomes in the GnomAD database, including 32,507 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 0.65 (32507 hom., cov: 32)
• Consequence: LOC105378641 XR_001737964.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 1 publications found

Genes affected

LOC105378641 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99139 AN: 151954 Hom.: 32484 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.652 AC: 99198 AN: 152072 Hom.: 32507 Cov.: 32 AF XY: 0.654 AC XY: 48619 AN XY: 74342

African (AFR) AF: 0.662 AC: 27459 AN: 41482

American (AMR) AF: 0.582 AC: 8896 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2500 AN: 3472

East Asian (EAS) AF: 0.621 AC: 3214 AN: 5172

South Asian (SAS) AF: 0.608 AC: 2935 AN: 4824

European-Finnish (FIN) AF: 0.689 AC: 7276 AN: 10562

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44680 AN: 67960

Other (OTH) AF: 0.662 AC: 1399 AN: 2112

Alfa AF: 0.652 Hom.: 25468

Bravo AF: 0.646

Asia WGS AF: 0.548 AC: 1906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.39
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs1016091; hg19: chr1-34924596;