4-156311579-A-G

Variant names:

• chr4-156311579-A-G
• rs10517639
• XR_939397.3:n.520-2646T>C

Variant summary

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

The XR_939397.3(LOC105377508):​n.520-2646T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,044 control chromosomes in the GnomAD database, including 3,139 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 0.20 (3139 hom., cov: 33)
• Consequence: LOC105377508 XR_939397.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530

Genes affected

LOC105377508 (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 (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377508	XR_939397.3	n.520-2646T>C		intron_variant	Intron 3 of 3
LOC105377508	XR_939398.3	n.503-2646T>C		intron_variant	Intron 3 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29980 AN: 151926 Hom.: 3125 Cov.: 33

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0515

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.198 AC: 30038 AN: 152044 Hom.: 3139 Cov.: 33 AF XY: 0.196 AC XY: 14558 AN XY: 74328

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.0519

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.191

Alfa AF: 0.188 Hom.: 3039

Bravo AF: 0.198

Asia WGS AF: 0.124 AC: 433 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	0.18
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517639; hg19: chr4-157232731; COSMIC: COSV50253585;