rs1354252

chr4-159577814-G-T

Variant summary

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

The XR_001741911.2(LOC107986324):n.76+37416G>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 0.245 in 152,020 control chromosomes in the GnomAD database, including 6,478 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 0.25 (6478 hom., cov: 31)
• Consequence: LOC107986324 XR_001741911.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

Genes affected

LOC107986324 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986324	XR_001741911.2	n.76+37416G>T		intron_variant, non_coding_transcript_variant
LOC107986324	XR_001741912.2	n.146+29311G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37208 AN: 151902 Hom.: 6445 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0499

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.0931

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.245 AC: 37294 AN: 152020 Hom.: 6478 Cov.: 31 AF XY: 0.238 AC XY: 17716 AN XY: 74330

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0498

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.0931

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.220

Alfa AF: 0.193 Hom.: 897

Bravo AF: 0.257

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.2
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1354252; hg19: chr4-160498966;