chr17-42438011-T-G

Position:

• chr17-42438011-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_934763.2(LOC102725238):​n.550+1619T>G variant causes a intron, non coding transcript 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: LOC102725238 XR_934763.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

Genes affected

LOC102725238 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC102725238	XR_934763.2	n.550+1619T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.745

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.730

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

Splicing

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

Publications

LitVar

Other links and lift over

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