chr17-42438011-T-G

Variant names:

• chr17-42438011-T-G
• rs4796659
• ENST00000723360.1:n.948+1619T>G

Variant summary

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

The ENST00000723360.1(ENSG00000294400):​n.948+1619T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.69 (20484 hom., cov: 15)
• Consequence: ENSG00000294400 ENST00000723360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 3 publications found

Genes affected

ENSG00000294400 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723360.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294400	ENST00000723360.1		n.948+1619T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.690 AC: 63454 AN: 91940 Hom.: 20464 Cov.: 15

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.690 AC: 63495 AN: 91972 Hom.: 20484 Cov.: 15 AF XY: 0.699 AC XY: 30156 AN XY: 43138

African (AFR) AF: 0.478 AC: 9499 AN: 19886

American (AMR) AF: 0.812 AC: 7777 AN: 9582

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2226 AN: 2850

East Asian (EAS) AF: 0.800 AC: 2572 AN: 3214

South Asian (SAS) AF: 0.745 AC: 1669 AN: 2240

European-Finnish (FIN) AF: 0.833 AC: 3504 AN: 4208

Middle Eastern (MID) AF: 0.852 AC: 121 AN: 142

European-Non Finnish (NFE) AF: 0.725 AC: 34774 AN: 47980

Other (OTH) AF: 0.730 AC: 908 AN: 1244

Alfa AF: 0.693 Hom.: 3580

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.11
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4796659; hg19: chr17-40590029; COSMIC: COSV71837882;