chr4-156311579-A-G

Variant names:

• chr4-156311579-A-G
• rs10517639
• ENST00000778470.1:n.267-22656A>G

Variant summary

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

The ENST00000778470.1(ENSG00000301356):​n.267-22656A>G 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: ENSG00000301356 ENST00000778470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530
• Publications: 2 publications found

Genes affected

ENSG00000301356 (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 (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
ENSG00000301356	ENST00000778470.1	n.267-22656A>G		intron_variant	Intron 2 of 4
ENSG00000301356	ENST00000778472.1	n.312-12516A>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.256 AC: 10605 AN: 41466

American (AMR) AF: 0.149 AC: 2276 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3470

East Asian (EAS) AF: 0.0519 AC: 268 AN: 5168

South Asian (SAS) AF: 0.182 AC: 875 AN: 4818

European-Finnish (FIN) AF: 0.191 AC: 2021 AN: 10586

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12801 AN: 67956

Other (OTH) AF: 0.191 AC: 403 AN: 2110

Alfa AF: 0.188 Hom.: 3476

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
PhyloP100		0.53

Splicing

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

Other links and lift over

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