10-44394204-G-T

Position:

• chr10-44394204-G-T

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 0.336 in 152,190 control chromosomes in the GnomAD database, including 9,791 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 0.34 (9791 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44394204G>T		intergenic_region
LOC107984179	XR_001747298.2	n.68-3953G>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51085 AN: 152072 Hom.: 9796 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.336 AC: 51088 AN: 152190 Hom.: 9791 Cov.: 33 AF XY: 0.342 AC XY: 25467 AN XY: 74406

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.378

Alfa AF: 0.378 Hom.: 15095

Bravo AF: 0.333

Asia WGS AF: 0.274 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1855531; hg19: chr10-44889652;