4-161237218-T-C

Variant summary

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

The XR_939409.1(LOC105377515):n.584-3117A>G 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 0.312 in 151,660 control chromosomes in the GnomAD database, including 7,613 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 0.31 (7613 hom., cov: 32)
• Consequence: LOC105377515 XR_939409.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

Genes affected

LOC105377515 (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 = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377515	XR_939409.1	n.584-3117A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47296 AN: 151542 Hom.: 7599 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.312 AC: 47345 AN: 151660 Hom.: 7613 Cov.: 32 AF XY: 0.305 AC XY: 22628 AN XY: 74142

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.311

Alfa AF: 0.291 Hom.: 6860

Bravo AF: 0.322

Asia WGS AF: 0.228 AC: 790 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.9
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517739; hg19: chr4-162158370;