rs1016091

chr1-34458995-C-T

Variant summary

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

The XR_001737964.2(LOC105378641):n.936-95G>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 0.652 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

Genes affected

LOC105378641 (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 (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378641	XR_001737964.2	n.936-95G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.662

Alfa AF: 0.650 Hom.: 21229

Bravo AF: 0.646

Asia WGS AF: 0.548 AC: 1906 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	1.3
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: rs1016091; hg19: chr1-34924596;