rs4876377

Positions:

• chr8-117474750-C-T

Variant summary

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

The XR_007061067.1(LOC105375716):​n.307-33538G>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 0.214 in 152,140 control chromosomes in the GnomAD database, including 4,411 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 0.21 (4411 hom., cov: 32)
• Consequence: LOC105375716 XR_007061067.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

LOC105375716 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375716	XR_007061067.1	n.307-33538G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32562 AN: 152022 Hom.: 4413 Cov.: 32

Gnomad AFR AF: 0.0662

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.0649

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.214 AC: 32561 AN: 152140 Hom.: 4411 Cov.: 32 AF XY: 0.210 AC XY: 15628 AN XY: 74366

Gnomad4 AFR AF: 0.0661

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.0651

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.229

Alfa AF: 0.250 Hom.: 662

Bravo AF: 0.204

Asia WGS AF: 0.170 AC: 593 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4876377; hg19: chr8-118486989;