rs4409785

Variant names:

• chr11-95578258-T-C
• rs4409785
• ENST00000648353.1:n.525+6050T>C

Variant summary

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

The ENST00000648353.1(ENSG00000285842):​n.525+6050T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,118 control chromosomes in the GnomAD database, including 1,715 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 0.13 (1715 hom., cov: 32)
• Consequence: ENSG00000285842 ENST00000648353.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 89 publications found

Genes affected

ENSG00000285842 (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 (SAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285842	ENST00000648353.1	n.525+6050T>C		intron_variant	Intron 3 of 4
ENSG00000306211	ENST00000816277.1	n.602+36802A>G		intron_variant	Intron 2 of 4
ENSG00000306211	ENST00000816278.1	n.218-8317A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19962 AN: 152000 Hom.: 1716 Cov.: 32

Gnomad AFR AF: 0.0327

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0939

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.131 AC: 19954 AN: 152118 Hom.: 1715 Cov.: 32 AF XY: 0.132 AC XY: 9834 AN XY: 74360

African (AFR) AF: 0.0326 AC: 1355 AN: 41542

American (AMR) AF: 0.126 AC: 1916 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3472

East Asian (EAS) AF: 0.0941 AC: 486 AN: 5164

South Asian (SAS) AF: 0.233 AC: 1124 AN: 4818

European-Finnish (FIN) AF: 0.174 AC: 1841 AN: 10588

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.174 AC: 11824 AN: 67956

Other (OTH) AF: 0.151 AC: 320 AN: 2114

Alfa AF: 0.162 Hom.: 10008

Bravo AF: 0.122

Asia WGS AF: 0.155 AC: 542 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	4.8
DANN	Benign	0.57
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4409785; hg19: chr11-95311422;