chr17-73734312-A-G

Variant names:

• chr17-73734312-A-G
• rs323413
• ENST00000734574.1:n.443-196T>C

Variant summary

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

The ENST00000734574.1(ENSG00000295965):​n.443-196T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,346 control chromosomes in the GnomAD database, including 23,666 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 0.53 (23666 hom., cov: 28)
• Consequence: ENSG00000295965 ENST00000734574.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 5 publications found

Genes affected

ENSG00000295965 (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 (AFR) allele frequency at 95% confidence interval = 0.801 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
ENSG00000295965	ENST00000734574.1	n.443-196T>C		intron_variant	Intron 3 of 3
ENSG00000295965	ENST00000734575.1	n.231-196T>C		intron_variant	Intron 2 of 2
ENSG00000295965	ENST00000734576.1	n.254-225T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80321 AN: 151226 Hom.: 23618 Cov.: 28

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.531 AC: 80430 AN: 151346 Hom.: 23666 Cov.: 28 AF XY: 0.528 AC XY: 39061 AN XY: 73950

African (AFR) AF: 0.808 AC: 33264 AN: 41164

American (AMR) AF: 0.489 AC: 7445 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1588 AN: 3468

East Asian (EAS) AF: 0.444 AC: 2268 AN: 5108

South Asian (SAS) AF: 0.495 AC: 2354 AN: 4754

European-Finnish (FIN) AF: 0.371 AC: 3899 AN: 10500

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.414 AC: 28063 AN: 67816

Other (OTH) AF: 0.506 AC: 1060 AN: 2096

Alfa AF: 0.427 Hom.: 20188

Bravo AF: 0.549

Asia WGS AF: 0.499 AC: 1734 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	0.28
DANN	Benign	0.25
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs323413; hg19: chr17-71730451;