17-41676424-G-A

Position:

• chr17-41676424-G-A

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 0.495 in 151,968 control chromosomes in the GnomAD database, including 19,096 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 0.49 (19096 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75145 AN: 151850 Hom.: 19074 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.495 AC: 75201 AN: 151968 Hom.: 19096 Cov.: 32 AF XY: 0.504 AC XY: 37464 AN XY: 74262

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.504

Alfa AF: 0.502 Hom.: 19709

Bravo AF: 0.477

Asia WGS AF: 0.611 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.57
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7219249; hg19: chr17-39832676;