1-44362853-G-T

Position:

• chr1-44362853-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0332 in 152,302 control chromosomes in the GnomAD database, including 109 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 0.033 (109 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0332 (5055/152302) while in subpopulation SAS AF= 0.0416 (201/4826). AF 95% confidence interval is 0.0392. There are 109 homozygotes in gnomad4. There are 2506 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 109 gene

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0332 AC: 5057 AN: 152184 Hom.: 109 Cov.: 32

Gnomad AFR AF: 0.0171

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0255

Gnomad ASJ AF: 0.0570

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0418

Gnomad FIN AF: 0.0577

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0404

Gnomad OTH AF: 0.0358

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

GnomAD4 genome AF: 0.0332 AC: 5055 AN: 152302 Hom.: 109 Cov.: 32 AF XY: 0.0337 AC XY: 2506 AN XY: 74470

Gnomad4 AFR AF: 0.0171

Gnomad4 AMR AF: 0.0255

Gnomad4 ASJ AF: 0.0570

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0416

Gnomad4 FIN AF: 0.0577

Gnomad4 NFE AF: 0.0404

Gnomad4 OTH AF: 0.0354

Alfa AF: 0.0358 Hom.: 65

Bravo AF: 0.0303

Asia WGS AF: 0.0160 AC: 54 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	0.67
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4660790; hg19: chr1-44828525;