rs7555879

Variant names:

• chr1-10829969-G-A
• rs7555879

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 0.0943 in 152,152 control chromosomes in the GnomAD database, including 1,036 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 0.094 (1036 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 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: 0.0942 AC: 14318 AN: 152034 Hom.: 1035 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.0452

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.0943 AC: 14345 AN: 152152 Hom.: 1036 Cov.: 32 AF XY: 0.0941 AC XY: 7000 AN XY: 74368

African (AFR) AF: 0.185 AC: 7684 AN: 41492

American (AMR) AF: 0.121 AC: 1847 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0259 AC: 90 AN: 3470

East Asian (EAS) AF: 0.132 AC: 679 AN: 5160

South Asian (SAS) AF: 0.0454 AC: 219 AN: 4824

European-Finnish (FIN) AF: 0.0520 AC: 551 AN: 10590

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0442 AC: 3005 AN: 68008

Other (OTH) AF: 0.0784 AC: 166 AN: 2116

Alfa AF: 0.0604 Hom.: 1851

Bravo AF: 0.104

Asia WGS AF: 0.0930 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.64
DANN	Benign	0.47
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs7555879; hg19: chr1-10890026;