rs2554297

Positions:

• chr1-59974513-G-A
• chr1-59974513-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 0.756 in 151,894 control chromosomes in the GnomAD database, including 43,511 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 0.76 (43511 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114802 AN: 151776 Hom.: 43462 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.756 AC: 114906 AN: 151894 Hom.: 43511 Cov.: 32 AF XY: 0.761 AC XY: 56481 AN XY: 74256

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.741

Alfa AF: 0.745 Hom.: 61566

Bravo AF: 0.753

Asia WGS AF: 0.796 AC: 2768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.76
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2554297; hg19: chr1-60440185;