rs436044

Variant names:

• chr16-64928745-C-T
• rs436044
• ENST00000722600.1:n.177+9852G>A

Variant summary

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

The ENST00000722600.1(ENSG00000294300):​n.177+9852G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.947 in 152,218 control chromosomes in the GnomAD database, including 68,274 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 0.95 (68274 hom., cov: 32)
• Consequence: ENSG00000294300 ENST00000722600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 1 publications found

Genes affected

ENSG00000294300 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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
ENSG00000294300	ENST00000722600.1	n.177+9852G>A		intron_variant	Intron 2 of 2
ENSG00000294300	ENST00000722601.1	n.72+11099G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.947 AC: 143972 AN: 152098 Hom.: 68222 Cov.: 32

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.947 AC: 144083 AN: 152218 Hom.: 68274 Cov.: 32 AF XY: 0.946 AC XY: 70374 AN XY: 74420

African (AFR) AF: 0.981 AC: 40789 AN: 41564

American (AMR) AF: 0.916 AC: 13981 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3345 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5171 AN: 5174

South Asian (SAS) AF: 0.960 AC: 4628 AN: 4820

European-Finnish (FIN) AF: 0.907 AC: 9616 AN: 10598

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63425 AN: 68012

Other (OTH) AF: 0.949 AC: 2007 AN: 2114

Alfa AF: 0.939 Hom.: 134074

Bravo AF: 0.949

Asia WGS AF: 0.976 AC: 3395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.54
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs436044; hg19: chr16-64962648;