17-41824648-T-C

Variant names:

• chr17-41824648-T-C
• rs9907244

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.260 AC: 10781 AN: 41514

American (AMR) AF: 0.397 AC: 6064 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2084 AN: 3470

East Asian (EAS) AF: 0.565 AC: 2916 AN: 5162

South Asian (SAS) AF: 0.528 AC: 2545 AN: 4824

European-Finnish (FIN) AF: 0.309 AC: 3274 AN: 10590

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29493 AN: 67972

Other (OTH) AF: 0.409 AC: 864 AN: 2112

Alfa AF: 0.426 Hom.: 39275

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
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs9907244; hg19: chr17-39980900;