rs7553380

Positions:

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

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 0.0921 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.0562

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0335

Gnomad4 NFE AF: 0.0573

Gnomad4 OTH AF: 0.0910

Alfa AF: 0.0608 Hom.: 430

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7553380; hg19: chr1-220626086;