1-104563876-T-C

Variant names:

• chr1-104563876-T-C
• rs7553985

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 0.369 in 151,798 control chromosomes in the GnomAD database, including 10,777 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 0.37 (10777 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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: 0.369 AC: 55944 AN: 151682 Hom.: 10767 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.369 AC: 56002 AN: 151798 Hom.: 10777 Cov.: 32 AF XY: 0.371 AC XY: 27547 AN XY: 74156

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.396

Alfa AF: 0.387 Hom.: 5808

Bravo AF: 0.371

Asia WGS AF: 0.503 AC: 1748 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	3.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7553985; hg19: chr1-105106498;