19-43539296-T-C

Variant names:

• chr19-43539296-T-C
• rs2030404

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 0.401 in 152,032 control chromosomes in the GnomAD database, including 12,623 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 0.40 (12623 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.439 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: 0.401 AC: 60960 AN: 151914 Hom.: 12615 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.401 AC: 61011 AN: 152032 Hom.: 12623 Cov.: 32 AF XY: 0.398 AC XY: 29611 AN XY: 74328

African (AFR) AF: 0.400 AC: 16561 AN: 41432

American (AMR) AF: 0.302 AC: 4610 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3468

East Asian (EAS) AF: 0.114 AC: 589 AN: 5172

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4818

European-Finnish (FIN) AF: 0.460 AC: 4859 AN: 10564

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30127 AN: 68000

Other (OTH) AF: 0.390 AC: 824 AN: 2112

Alfa AF: 0.413 Hom.: 17511

Bravo AF: 0.384

Asia WGS AF: 0.258 AC: 903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.55
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs2030404; hg19: chr19-44043448;