19-7748977-G-A

Position:

• chr19-7748977-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.271 in 152,094 control chromosomes in the GnomAD database, including 6,905 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 0.27 (6905 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.7748977G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41225 AN: 151976 Hom.: 6901 Cov.: 32

Gnomad AFR AF: 0.0663

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.271 AC: 41230 AN: 152094 Hom.: 6905 Cov.: 32 AF XY: 0.275 AC XY: 20471 AN XY: 74344

Gnomad4 AFR AF: 0.0661

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.292

Alfa AF: 0.295 Hom.: 1164

Bravo AF: 0.255

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.74
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4804804; hg19: chr19-7813863;