19-40983946-T-C

Variant names:

• chr19-40983946-T-C
• rs892216

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 0.408 in 151,880 control chromosomes in the GnomAD database, including 13,193 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 0.41 (13193 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.509 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: 0.408 AC: 61933 AN: 151762 Hom.: 13158 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.408 AC: 62025 AN: 151880 Hom.: 13193 Cov.: 31 AF XY: 0.410 AC XY: 30460 AN XY: 74222

African (AFR) AF: 0.515 AC: 21285 AN: 41370

American (AMR) AF: 0.415 AC: 6335 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3466

East Asian (EAS) AF: 0.444 AC: 2286 AN: 5154

South Asian (SAS) AF: 0.370 AC: 1782 AN: 4822

European-Finnish (FIN) AF: 0.403 AC: 4253 AN: 10558

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.348 AC: 23659 AN: 67928

Other (OTH) AF: 0.382 AC: 806 AN: 2110

Alfa AF: 0.385 Hom.: 1451

Bravo AF: 0.416

Asia WGS AF: 0.392 AC: 1367 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	2.0
DANN	Benign	0.34
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs892216; hg19: chr19-41489851;