rs11204553

Positions:

• chr1-247906610-G-A
• chr1-247906610-G-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 0.734 in 152,090 control chromosomes in the GnomAD database, including 42,348 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 0.73 (42348 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 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: 0.734 AC: 111571 AN: 151972 Hom.: 42351 Cov.: 33

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.734 AC: 111609 AN: 152090 Hom.: 42348 Cov.: 33 AF XY: 0.734 AC XY: 54571 AN XY: 74346

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.765

Alfa AF: 0.806 Hom.: 62011

Bravo AF: 0.726

Asia WGS AF: 0.835 AC: 2902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.94
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11204553; hg19: chr1-248069912;