rs10517704

Variant names:

• chr4-159656869-A-G
• rs10517704
• XR_001741911.2:n.77-72474A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-159656869-A-G
• chr4-159656869-A-T

Variant summary

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

The XR_001741911.2(LOC107986324):​n.77-72474A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 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: 0.455 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

African (AFR) AF: 0.469 AC: 19448 AN: 41476

American (AMR) AF: 0.351 AC: 5361 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1597 AN: 3468

East Asian (EAS) AF: 0.154 AC: 797 AN: 5184

South Asian (SAS) AF: 0.484 AC: 2331 AN: 4820

European-Finnish (FIN) AF: 0.422 AC: 4463 AN: 10568

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33570 AN: 67968

Other (OTH) AF: 0.476 AC: 1006 AN: 2112

Alfa AF: 0.478 Hom.: 65755

Bravo AF: 0.447

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.85
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10517704; hg19: chr4-160578021;