1-202960413-C-G

Variant names:

• chr1-202960413-C-G
• rs7523903

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 0.0803 in 152,224 control chromosomes in the GnomAD database, including 1,231 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 0.080 (1231 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 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: 0.0801 AC: 12181 AN: 152106 Hom.: 1217 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0360

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00663

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0803 AC: 12228 AN: 152224 Hom.: 1231 Cov.: 32 AF XY: 0.0809 AC XY: 6020 AN XY: 74418

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.0362

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.0982

Gnomad4 FIN AF: 0.00311

Gnomad4 NFE AF: 0.00664

Gnomad4 OTH AF: 0.0724

Alfa AF: 0.00926 Hom.: 11

Bravo AF: 0.0884

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.50
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7523903; hg19: chr1-202929541;