17-45607704-T-C

Variant names:

• chr17-45607704-T-C
• rs9894846
• ENST00000732911.1:n.377-831T>C

Variant summary

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

The ENST00000732911.1(ENSG00000295828):​n.377-831T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.982 in 151,490 control chromosomes in the GnomAD database, including 73,070 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 0.98 (73070 hom., cov: 29)
• Consequence: ENSG00000295828 ENST00000732911.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852
• Publications: 1 publications found

Genes affected

ENSG00000295828 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 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
ENSG00000295828	ENST00000732911.1	n.377-831T>C		intron_variant	Intron 3 of 3
ENSG00000295828	ENST00000732912.1	n.442-829T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.982 AC: 148630 AN: 151372 Hom.: 73015 Cov.: 29

Gnomad AFR AF: 0.938

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.992

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.987

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.986

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

GnomAD4 genome AF: 0.982 AC: 148744 AN: 151490 Hom.: 73070 Cov.: 29 AF XY: 0.982 AC XY: 72658 AN XY: 73964

African (AFR) AF: 0.938 AC: 38629 AN: 41200

American (AMR) AF: 0.992 AC: 15052 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3467 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5129 AN: 5130

South Asian (SAS) AF: 1.00 AC: 4789 AN: 4790

European-Finnish (FIN) AF: 1.00 AC: 10481 AN: 10482

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67925 AN: 67946

Other (OTH) AF: 0.986 AC: 2072 AN: 2102

Alfa AF: 0.994 Hom.: 3878

Bravo AF: 0.979

Asia WGS AF: 0.997 AC: 3466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.3
DANN	Benign	0.29
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs9894846; hg19: chr17-43685070;