rs11935505

Variant names:

• chr4-144305270-G-A
• rs11935505
• ENST00000649263.1:n.*44-22084C>T

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.*44-22084C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,012 control chromosomes in the GnomAD database, including 2,489 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 0.14 (2489 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.765
• Publications: 1 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.315-22084C>T		intron_variant	Intron 3 of 7
LOC105377462	XR_939273.3	n.241-22084C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.*44-22084C>T		intron_variant	Intron 5 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000648340.1	n.215-22084C>T		intron_variant	Intron 2 of 5
ENSG00000285783	ENST00000650526.1	n.299-22084C>T		intron_variant	Intron 3 of 14
GUSBP5	ENST00000651102.1	n.1926-11541G>A		intron_variant	Intron 12 of 14

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21291 AN: 151894 Hom.: 2483 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0447

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0534

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.140 AC: 21332 AN: 152012 Hom.: 2489 Cov.: 32 AF XY: 0.138 AC XY: 10270 AN XY: 74308

African (AFR) AF: 0.328 AC: 13599 AN: 41414

American (AMR) AF: 0.135 AC: 2061 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3470

East Asian (EAS) AF: 0.146 AC: 755 AN: 5170

South Asian (SAS) AF: 0.0387 AC: 187 AN: 4826

European-Finnish (FIN) AF: 0.0447 AC: 474 AN: 10594

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0534 AC: 3632 AN: 67964

Other (OTH) AF: 0.130 AC: 274 AN: 2110

Alfa AF: 0.0720 Hom.: 1003

Bravo AF: 0.157

Asia WGS AF: 0.110 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	1.8
DANN	Benign	0.59
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs11935505; hg19: chr4-145226422;