17-42438011-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102725238	XR_001752890.3	n.500+1619T>G		intron_variant	Intron 3 of 3
LOC102725238	XR_002958124.2	n.555+1619T>G		intron_variant	Intron 2 of 2
LOC102725238	XR_007065758.1	n.384+1619T>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294400	ENST00000723360.1	n.948+1619T>G		intron_variant	Intron 3 of 3

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 v4.3

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;