7-130719948-G-A

Variant names:

• chr7-130719948-G-A
• rs4067228

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 0.56 in 151,904 control chromosomes in the GnomAD database, including 23,996 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 0.56 (23996 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.578 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: 0.560 AC: 84995 AN: 151786 Hom.: 23978 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.560 AC: 85051 AN: 151904 Hom.: 23996 Cov.: 31 AF XY: 0.559 AC XY: 41459 AN XY: 74216

African (AFR) AF: 0.572 AC: 23684 AN: 41400

American (AMR) AF: 0.588 AC: 8978 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2027 AN: 3464

East Asian (EAS) AF: 0.538 AC: 2775 AN: 5162

South Asian (SAS) AF: 0.512 AC: 2460 AN: 4806

European-Finnish (FIN) AF: 0.545 AC: 5749 AN: 10552

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37407 AN: 67948

Other (OTH) AF: 0.570 AC: 1200 AN: 2104

Alfa AF: 0.554 Hom.: 70497

Bravo AF: 0.565

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.80
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4067228; hg19: chr7-130404776;