chr17-44010885-T-C

Position:

• chr17-44010885-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 0.937 in 152,220 control chromosomes in the GnomAD database, including 66,895 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 0.94 (66895 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797

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 (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44010885T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.937 AC: 142535 AN: 152102 Hom.: 66838 Cov.: 31

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.958

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.937 AC: 142650 AN: 152220 Hom.: 66895 Cov.: 31 AF XY: 0.940 AC XY: 69982 AN XY: 74434

Gnomad4 AFR AF: 0.903

Gnomad4 AMR AF: 0.960

Gnomad4 ASJ AF: 0.958

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.989

Gnomad4 FIN AF: 0.950

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.952

Alfa AF: 0.937 Hom.: 7772

Bravo AF: 0.935

Asia WGS AF: 0.986 AC: 3429 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	0.59
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs228776; hg19: chr17-42088253;