chr17-79849763-G-T

Position:

• chr17-79849763-G-T

Variant summary

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

The variant allele was found at a frequency of 0.417 in 152,108 control chromosomes in the GnomAD database, including 14,689 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 0.42 (14689 hom., cov: 33)
  • Exomes 𝑓: 0.30 (0 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.79849763G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000262343	ENST00000570408.1	n.213+135C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63460 AN: 151980 Hom.: 14684 Cov.: 33

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.435

GnomAD4 exome AF: 0.300 AC: 3 AN: 10 Hom.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 AMR exome AF: 0.00

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.417 AC: 63480 AN: 152098 Hom.: 14689 Cov.: 33 AF XY: 0.417 AC XY: 30982 AN XY: 74352

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.430

Alfa AF: 0.457 Hom.: 7048

Bravo AF: 0.401

Asia WGS AF: 0.199 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.032
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1622986; hg19: chr17-77823562;