rs7555879

Variant names:

• chr1-10829969-G-A
• rs7555879

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 0.0943 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0942 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

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0259

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.0454

Gnomad4 FIN AF: 0.0520

Gnomad4 NFE AF: 0.0442

Gnomad4 OTH AF: 0.0784

Alfa AF: 0.0522 Hom.: 637

Bravo AF: 0.104

Asia WGS AF: 0.0930 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7555879; hg19: chr1-10890026;