rs957334

Positions:

• chr1-94563425-A-C

Variant summary

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

The XR_001738160.3(LOC105378861):​n.323A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,982 control chromosomes in the GnomAD database, including 19,862 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 0.51 (19862 hom., cov: 32)
• Consequence: LOC105378861 XR_001738160.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

Genes affected

LOC105378861 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378861	XR_001738160.3	n.323A>C		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77439 AN: 151864 Hom.: 19837 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.510 AC: 77525 AN: 151982 Hom.: 19862 Cov.: 32 AF XY: 0.509 AC XY: 37817 AN XY: 74256

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.526

Alfa AF: 0.484 Hom.: 5948

Bravo AF: 0.520

Asia WGS AF: 0.479 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
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: rs957334; hg19: chr1-95028981;