rs4976139

chr5-67936035-G-A

Variant summary

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

The XR_948392.3(LOC105379007):n.720+10354G>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 0.302 in 152,044 control chromosomes in the GnomAD database, including 7,121 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 0.30 (7121 hom., cov: 32)
• Consequence: LOC105379007 XR_948392.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943

Genes affected

LOC105379007 (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 (AMR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379007	XR_948392.3	n.720+10354G>A		intron_variant, non_coding_transcript_variant
LOC105379007	XR_002956213.2	n.525+10354G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45920 AN: 151926 Hom.: 7119 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.0774

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.302 AC: 45947 AN: 152044 Hom.: 7121 Cov.: 32 AF XY: 0.301 AC XY: 22348 AN XY: 74330

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.0778

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.320

Alfa AF: 0.310 Hom.: 15148

Bravo AF: 0.305

Asia WGS AF: 0.176 AC: 616 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	1.3
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4976139; hg19: chr5-67231863;