4-159567154-G-T

Variant names:

• chr4-159567154-G-T
• rs9992703
• XR_001741911.2:n.76+26756G>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+26756G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,888 control chromosomes in the GnomAD database, including 16,132 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 (16132 hom., cov: 31)
• Consequence: LOC107986324 XR_001741911.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

Genes affected

LOC107986324 (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 (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986324	XR_001741911.2	n.76+26756G>T		intron_variant	Intron 1 of 2
LOC107986324	XR_001741912.2	n.146+18651G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68620 AN: 151770 Hom.: 16114 Cov.: 31

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.452 AC: 68686 AN: 151888 Hom.: 16132 Cov.: 31 AF XY: 0.458 AC XY: 34017 AN XY: 74230

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.465

Alfa AF: 0.437 Hom.: 2131

Bravo AF: 0.465

Asia WGS AF: 0.547 AC: 1900 AN: 3478

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	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9992703; hg19: chr4-160488306;