chr7-19009765-G-A

Position:

• chr7-19009765-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.193 in 151,892 control chromosomes in the GnomAD database, including 2,975 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 0.19 (2975 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.19009765G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29224 AN: 151774 Hom.: 2958 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.193 AC: 29266 AN: 151892 Hom.: 2975 Cov.: 33 AF XY: 0.196 AC XY: 14549 AN XY: 74244

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.202

Alfa AF: 0.171 Hom.: 1846

Bravo AF: 0.193

Asia WGS AF: 0.339 AC: 1177 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	18
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2107595; hg19: chr7-19049388;