rs11645416

chr16-51426756-A-C

Variant summary

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

The ENST00000643262.1(ENSG00000260850):n.399+68346T>G 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 0.139 in 152,128 control chromosomes in the GnomAD database, including 1,974 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 (1974 hom., cov: 32)
• Consequence: ENST00000643262.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723323	XR_933558.3	n.376-22128T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000643262.1	n.399+68346T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21116 AN: 152010 Hom.: 1974 Cov.: 32

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.139 AC: 21110 AN: 152128 Hom.: 1974 Cov.: 32 AF XY: 0.137 AC XY: 10159 AN XY: 74362

Gnomad4 AFR AF: 0.0338

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0831

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.171

Alfa AF: 0.174 Hom.: 1248

Bravo AF: 0.136

Asia WGS AF: 0.0460 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.0
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11645416; hg19: chr16-51460667;