rs7553007

Variant names:

• chr1-159728759-G-A
• rs7553007

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 0.318 in 151,952 control chromosomes in the GnomAD database, including 8,117 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 0.32 (8117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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: 0.318 AC: 48297 AN: 151834 Hom.: 8110 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.318 AC: 48323 AN: 151952 Hom.: 8117 Cov.: 32 AF XY: 0.322 AC XY: 23888 AN XY: 74244

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.336

Alfa AF: 0.339 Hom.: 17348

Bravo AF: 0.314

Asia WGS AF: 0.440 AC: 1531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.21
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7553007; hg19: chr1-159698549;