rs7553380

Variant names:

• chr1-220452744-A-G
• rs7553380

Your query was ambiguous. Multiple possible variants found:

• chr1-220452744-A-G
• chr1-220452744-A-T

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 0.0921 in 152,150 control chromosomes in the GnomAD database, including 874 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 0.092 (874 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 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: 0.0919 AC: 13969 AN: 152030 Hom.: 869 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0563

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0335

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.0881

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

GnomAD4 genome AF: 0.0921 AC: 14018 AN: 152150 Hom.: 874 Cov.: 32 AF XY: 0.0916 AC XY: 6811 AN XY: 74384

African (AFR) AF: 0.166 AC: 6888 AN: 41492

American (AMR) AF: 0.0562 AC: 858 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3468

East Asian (EAS) AF: 0.111 AC: 575 AN: 5176

South Asian (SAS) AF: 0.153 AC: 735 AN: 4818

European-Finnish (FIN) AF: 0.0335 AC: 355 AN: 10588

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0573 AC: 3894 AN: 68012

Other (OTH) AF: 0.0910 AC: 192 AN: 2110

Alfa AF: 0.0648 Hom.: 611

Bravo AF: 0.0948

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.74
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7553380; hg19: chr1-220626086;