rs11644034

Variant names:

• chr16-85939006-G-A
• rs11644034
• ENST00000645383.1:n.394-6410G>A

Variant summary

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

The ENST00000645383.1(ENSG00000285163):​n.394-6410G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,246 control chromosomes in the GnomAD database, including 2,992 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 0.19 (2992 hom., cov: 33)
• Consequence: ENSG00000285163 ENST00000645383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 36 publications found

Genes affected

ENSG00000285163 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 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
ENSG00000285163	ENST00000645383.1	n.394-6410G>A		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646214.1	n.78-6410G>A		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646986.2	n.715+2995G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28687 AN: 152128 Hom.: 2992 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.0926

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.189 AC: 28702 AN: 152246 Hom.: 2992 Cov.: 33 AF XY: 0.187 AC XY: 13945 AN XY: 74422

African (AFR) AF: 0.134 AC: 5589 AN: 41560

American (AMR) AF: 0.206 AC: 3159 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0916 AC: 318 AN: 3472

East Asian (EAS) AF: 0.0928 AC: 481 AN: 5182

South Asian (SAS) AF: 0.0744 AC: 359 AN: 4828

European-Finnish (FIN) AF: 0.283 AC: 2993 AN: 10588

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15257 AN: 67998

Other (OTH) AF: 0.167 AC: 352 AN: 2114

Alfa AF: 0.208 Hom.: 14606

Bravo AF: 0.182

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.82
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs11644034; hg19: chr16-85972612;