1-44362853-G-T

Variant names:

• chr1-44362853-G-T
• rs4660790

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 109 gene

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: 0.0332 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

African (AFR) AF: 0.0171 AC: 709 AN: 41580

American (AMR) AF: 0.0255 AC: 390 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0570 AC: 198 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0416 AC: 201 AN: 4826

European-Finnish (FIN) AF: 0.0577 AC: 613 AN: 10618

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0404 AC: 2750 AN: 68012

Other (OTH) AF: 0.0354 AC: 75 AN: 2116

Alfa AF: 0.0363 Hom.: 68

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
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs4660790; hg19: chr1-44828525;