rs1199038

Variant names:

• chr1-43334330-C-T
• rs1199038

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 0.298 in 152,050 control chromosomes in the GnomAD database, including 7,494 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 0.30 (7494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.369 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: 0.298 AC: 45273 AN: 151934 Hom.: 7493 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.0743

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.298 AC: 45299 AN: 152050 Hom.: 7494 Cov.: 32 AF XY: 0.294 AC XY: 21858 AN XY: 74318

African (AFR) AF: 0.176 AC: 7284 AN: 41498

American (AMR) AF: 0.360 AC: 5500 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1410 AN: 3470

East Asian (EAS) AF: 0.0743 AC: 385 AN: 5184

South Asian (SAS) AF: 0.138 AC: 667 AN: 4820

European-Finnish (FIN) AF: 0.332 AC: 3496 AN: 10524

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.373 AC: 25342 AN: 67978

Other (OTH) AF: 0.352 AC: 744 AN: 2112

Alfa AF: 0.356 Hom.: 13079

Bravo AF: 0.296

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.60
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1199038; hg19: chr1-43800001;