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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986324	XR_001741911.2	n.77-72474A>G		intron_variant	Intron 1 of 2
LOC107986324	XR_001741912.2	n.147-72474A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

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 v4.3

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;