rs7550380

Variant names:

• chr1-186695373-G-T
• rs7550380

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 0.218 in 151,976 control chromosomes in the GnomAD database, including 4,658 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 0.22 (4658 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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: 0.218 AC: 33095 AN: 151858 Hom.: 4638 Cov.: 31

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.0488

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.218 AC: 33154 AN: 151976 Hom.: 4658 Cov.: 31 AF XY: 0.213 AC XY: 15806 AN XY: 74296

African (AFR) AF: 0.391 AC: 16169 AN: 41384

American (AMR) AF: 0.186 AC: 2848 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 808 AN: 3466

East Asian (EAS) AF: 0.0485 AC: 251 AN: 5170

South Asian (SAS) AF: 0.164 AC: 791 AN: 4820

European-Finnish (FIN) AF: 0.0869 AC: 919 AN: 10578

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.158 AC: 10754 AN: 67972

Other (OTH) AF: 0.224 AC: 473 AN: 2110

Alfa AF: 0.197 Hom.: 470

Bravo AF: 0.234

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.13
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7550380; hg19: chr1-186664505; COSMIC: COSV107159217;