rs10517704

chr4-159656869-A-Gchr4-159656869-A-T

Variant summary

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

The XR_001741911.2(LOC107986324):n.77-72474A>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 0.455 in 152,086 control chromosomes in the GnomAD database, including 16,153 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 0.45 (16153 hom., cov: 33)
• Consequence: LOC107986324 XR_001741911.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427

Genes affected

LOC107986324 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986324	XR_001741911.2	n.77-72474A>G		intron_variant, non_coding_transcript_variant
LOC107986324	XR_001741912.2	n.147-72474A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69142 AN: 151968 Hom.: 16147 Cov.: 33

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.455 AC: 69144 AN: 152086 Hom.: 16153 Cov.: 33 AF XY: 0.447 AC XY: 33265 AN XY: 74358

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.476

Alfa AF: 0.483 Hom.: 28869

Bravo AF: 0.447

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.2
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517704; hg19: chr4-160578021;