chr7-20239019-G-T

Position:

• chr7-20239019-G-T

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 0.0722 in 152,116 control chromosomes in the GnomAD database, including 695 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 0.072 (695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0719 AC: 10923 AN: 152000 Hom.: 686 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.0426

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0344

Gnomad OTH AF: 0.0640

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

GnomAD4 genome AF: 0.0722 AC: 10976 AN: 152116 Hom.: 695 Cov.: 32 AF XY: 0.0718 AC XY: 5339 AN XY: 74356

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0410

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0334

Gnomad4 FIN AF: 0.0426

Gnomad4 NFE AF: 0.0344

Gnomad4 OTH AF: 0.0695

Alfa AF: 0.0421 Hom.: 104

Bravo AF: 0.0760

Asia WGS AF: 0.0560 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7806550; hg19: chr7-20278642;