4-159840214-C-G

Variant names:

• chr4-159840214-C-G
• rs10517710
• XR_001741911.2:n.175+110773C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001741911.2(LOC107986324):​n.175+110773C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: LOC107986324 XR_001741911.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 0 publications found

Genes affected

LOC107986324 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.770 AC: 31586 AN: 40996

American (AMR) AF: 0.927 AC: 13952 AN: 15050

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3314 AN: 3466

East Asian (EAS) AF: 0.781 AC: 3915 AN: 5016

South Asian (SAS) AF: 0.935 AC: 4486 AN: 4800

European-Finnish (FIN) AF: 0.992 AC: 10166 AN: 10244

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.973 AC: 66082 AN: 67902

Other (OTH) AF: 0.917 AC: 1921 AN: 2096

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.036
DANN	Benign	0.66
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10517710; hg19: chr4-160761366;