chr17-40107944-A-G

Variant names:

• chr17-40107944-A-G
• rs16965644

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 0.155 in 152,082 control chromosomes in the GnomAD database, including 2,368 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 0.16 (2368 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

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 (AFR) allele frequency at 95% confidence interval = 0.271 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: 0.155 AC: 23532 AN: 151964 Hom.: 2354 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0250

Gnomad FIN AF: 0.0892

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.155 AC: 23585 AN: 152082 Hom.: 2368 Cov.: 31 AF XY: 0.151 AC XY: 11207 AN XY: 74338

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0253

Gnomad4 FIN AF: 0.0892

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.135

Alfa AF: 0.129 Hom.: 1839

Bravo AF: 0.164

Asia WGS AF: 0.0370 AC: 130 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	0.39
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16965644; hg19: chr17-38264197;