4-159840214-C-G

Position:

• chr4-159840214-C-G

Variant summary

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

The variant allele was found at a frequency of 0.906 in 150,772 control chromosomes in the GnomAD database, including 62,494 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 0.91 (62494 hom., cov: 27)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

Genes affected

(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 (NFE) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.159840214C>G		intergenic_region
LOC107986324	XR_001741911.2	n.175+110773C>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.906 AC: 136482 AN: 150654 Hom.: 62467 Cov.: 27

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.906 AC: 136567 AN: 150772 Hom.: 62494 Cov.: 27 AF XY: 0.907 AC XY: 66616 AN XY: 73474

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.927

Gnomad4 ASJ AF: 0.956

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.935

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.973

Gnomad4 OTH AF: 0.917

Alfa AF: 0.956 Hom.: 3367

Bravo AF: 0.895

Asia WGS AF: 0.881 AC: 3066 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	0.036
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517710; hg19: chr4-160761366;