7-18054664-A-G

Variant names:

• chr7-18054664-A-G
• rs1961969

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 0.236 in 151,994 control chromosomes in the GnomAD database, including 4,745 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 0.24 (4745 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35822 AN: 151876 Hom.: 4738 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.236 AC: 35850 AN: 151994 Hom.: 4745 Cov.: 32 AF XY: 0.244 AC XY: 18101 AN XY: 74310

African (AFR) AF: 0.203 AC: 8407 AN: 41492

American (AMR) AF: 0.212 AC: 3233 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3470

East Asian (EAS) AF: 0.566 AC: 2925 AN: 5166

South Asian (SAS) AF: 0.415 AC: 1999 AN: 4822

European-Finnish (FIN) AF: 0.299 AC: 3142 AN: 10518

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14723 AN: 67954

Other (OTH) AF: 0.234 AC: 493 AN: 2110

Alfa AF: 0.236 Hom.: 2980

Bravo AF: 0.227

Asia WGS AF: 0.434 AC: 1504 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.2
DANN	Benign	0.95
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1961969; hg19: chr7-18094287;