rs4409785

Positions:

• chr11-95578258-T-C

Variant summary

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

The ENST00000648353.1(ENSG00000285842):​n.525+6050T>C variant causes a intron, non coding transcript 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: ENST00000648353.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

Genes affected

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648353.1	n.525+6050T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0326

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.0941

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.151

Alfa AF: 0.172 Hom.: 5083

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4409785; hg19: chr11-95311422;