17-41824648-T-C

Position:

• chr17-41824648-T-C

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 0.385 in 152,140 control chromosomes in the GnomAD database, including 11,978 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 0.39 (11978 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.926

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58594 AN: 152022 Hom.: 11976 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.385 AC: 58597 AN: 152140 Hom.: 11978 Cov.: 33 AF XY: 0.384 AC XY: 28582 AN XY: 74386

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.409

Alfa AF: 0.439 Hom.: 26553

Bravo AF: 0.383

Asia WGS AF: 0.487 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9907244; hg19: chr17-39980900;