chr19-1101993-A-G

Variant names:

• chr19-1101993-A-G
• rs757228

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 0.538 in 151,920 control chromosomes in the GnomAD database, including 22,099 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 0.54 (22099 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.89
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 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: 0.537 AC: 81575 AN: 151802 Hom.: 22058 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.538 AC: 81672 AN: 151920 Hom.: 22099 Cov.: 31 AF XY: 0.546 AC XY: 40521 AN XY: 74264

African (AFR) AF: 0.597 AC: 24741 AN: 41434

American (AMR) AF: 0.586 AC: 8937 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1682 AN: 3472

East Asian (EAS) AF: 0.548 AC: 2830 AN: 5166

South Asian (SAS) AF: 0.552 AC: 2661 AN: 4820

European-Finnish (FIN) AF: 0.610 AC: 6429 AN: 10542

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32518 AN: 67918

Other (OTH) AF: 0.523 AC: 1102 AN: 2106

Alfa AF: 0.495 Hom.: 62765

Bravo AF: 0.535

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.12
DANN	Benign	0.65
PhyloP100		-4.9

Splicing

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

Other links and lift over

dbSNP: rs757228; hg19: chr19-1101992;