7-20239019-G-T

Variant names:

• chr7-20239019-G-T
• rs7806550

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 0.0722 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.173 AC: 7193 AN: 41478

American (AMR) AF: 0.0410 AC: 626 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3468

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5186

South Asian (SAS) AF: 0.0334 AC: 161 AN: 4820

European-Finnish (FIN) AF: 0.0426 AC: 451 AN: 10580

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0344 AC: 2337 AN: 68000

Other (OTH) AF: 0.0695 AC: 147 AN: 2116

Alfa AF: 0.0411 Hom.: 362

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
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs7806550; hg19: chr7-20278642;