chr1-1330080-T-C

Variant names:

• chr1-1330080-T-C
• rs35744813

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.762 in 151,522 control chromosomes in the GnomAD database, including 48,112 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 0.76 (48112 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.482
• Publications: 27 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.927 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: 0.763 AC: 115466 AN: 151400 Hom.: 48117 Cov.: 34

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.949

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.878

Gnomad NFE AF: 0.934

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.762 AC: 115481 AN: 151522 Hom.: 48112 Cov.: 34 AF XY: 0.764 AC XY: 56548 AN XY: 74062

African (AFR) AF: 0.392 AC: 16214 AN: 41366

American (AMR) AF: 0.838 AC: 12785 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3146 AN: 3462

East Asian (EAS) AF: 0.812 AC: 4172 AN: 5138

South Asian (SAS) AF: 0.839 AC: 4032 AN: 4804

European-Finnish (FIN) AF: 0.873 AC: 9157 AN: 10486

Middle Eastern (MID) AF: 0.870 AC: 254 AN: 292

European-Non Finnish (NFE) AF: 0.934 AC: 63209 AN: 67710

Other (OTH) AF: 0.789 AC: 1656 AN: 2098

Alfa AF: 0.838 Hom.: 6956

Bravo AF: 0.744

Asia WGS AF: 0.771 AC: 2684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
DANN	Benign	0.15
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs35744813; hg19: chr1-1265460;