rs4915318

chr1-196927958-C-Achr1-196927958-C-Gchr1-196927958-C-T

Variant summary

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

The XR_007066779.1(LOC105371675):n.258-4947G>T 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 0.235 in 150,974 control chromosomes in the GnomAD database, including 5,935 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 0.24 (5935 hom., cov: 31)
• Consequence: LOC105371675 XR_007066779.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199

Genes affected

LOC105371675 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371675	XR_007066779.1	n.258-4947G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35508 AN: 150862 Hom.: 5926 Cov.: 31

Gnomad AFR AF: 0.0776

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.235 AC: 35525 AN: 150974 Hom.: 5935 Cov.: 31 AF XY: 0.246 AC XY: 18141 AN XY: 73756

Gnomad4 AFR AF: 0.0776

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.256

Alfa AF: 0.201 Hom.: 1253

Bravo AF: 0.240

Asia WGS AF: 0.507 AC: 1760 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.0
Dann	Benign	0.13

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4915318; hg19: chr1-196897088;