rs7554500

Variant names:

• chr1-147849353-A-G
• rs7554500

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 0.0231 in 152,352 control chromosomes in the GnomAD database, including 56 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 0.023 (56 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0731 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: 0.0231 AC: 3511 AN: 152234 Hom.: 56 Cov.: 32

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0183

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.0796

Gnomad SAS AF: 0.0475

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0167

Gnomad OTH AF: 0.0181

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

GnomAD4 genome AF: 0.0231 AC: 3523 AN: 152352 Hom.: 56 Cov.: 32 AF XY: 0.0241 AC XY: 1799 AN XY: 74510

African (AFR) AF: 0.0284 AC: 1182 AN: 41574

American (AMR) AF: 0.0182 AC: 279 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00835 AC: 29 AN: 3472

East Asian (EAS) AF: 0.0794 AC: 412 AN: 5188

South Asian (SAS) AF: 0.0482 AC: 233 AN: 4834

European-Finnish (FIN) AF: 0.0184 AC: 196 AN: 10626

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0167 AC: 1139 AN: 68042

Other (OTH) AF: 0.0203 AC: 43 AN: 2116

Alfa AF: 0.0212 Hom.: 11

Bravo AF: 0.0228

Asia WGS AF: 0.0780 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.0
DANN	Benign	0.90
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs7554500; hg19: chr1-147321489;