4-165359528-T-C

Variant names:

• chr4-165359528-T-C
• rs4690810
• XR_939416.2:n.570-1562T>C

Variant summary

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

The XR_939416.2(LOC105377519):​n.570-1562T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,008 control chromosomes in the GnomAD database, including 10,609 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 0.37 (10609 hom., cov: 33)
• Consequence: LOC105377519 XR_939416.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 2 publications found

Genes affected

LOC105377519 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377519	XR_939416.2	n.570-1562T>C		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56153 AN: 151890 Hom.: 10612 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.369 AC: 56165 AN: 152008 Hom.: 10609 Cov.: 33 AF XY: 0.367 AC XY: 27251 AN XY: 74280

African (AFR) AF: 0.379 AC: 15706 AN: 41454

American (AMR) AF: 0.326 AC: 4989 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1338 AN: 3470

East Asian (EAS) AF: 0.573 AC: 2965 AN: 5172

South Asian (SAS) AF: 0.444 AC: 2142 AN: 4824

European-Finnish (FIN) AF: 0.342 AC: 3605 AN: 10546

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24231 AN: 67946

Other (OTH) AF: 0.377 AC: 793 AN: 2106

Alfa AF: 0.237 Hom.: 579

Bravo AF: 0.368

Asia WGS AF: 0.448 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6
DANN	Benign	0.79
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs4690810; hg19: chr4-166280680;