1-102003830-T-C

Variant names:

• chr1-102003830-T-C
• rs6657751

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.449 in 152,038 control chromosomes in the GnomAD database, including 15,758 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 0.45 (15758 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 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: 0.449 AC: 68225 AN: 151920 Hom.: 15759 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.449 AC: 68247 AN: 152038 Hom.: 15758 Cov.: 32 AF XY: 0.443 AC XY: 32944 AN XY: 74332

African (AFR) AF: 0.394 AC: 16350 AN: 41448

American (AMR) AF: 0.533 AC: 8148 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2142 AN: 3470

East Asian (EAS) AF: 0.567 AC: 2931 AN: 5172

South Asian (SAS) AF: 0.457 AC: 2204 AN: 4826

European-Finnish (FIN) AF: 0.280 AC: 2957 AN: 10568

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31831 AN: 67956

Other (OTH) AF: 0.529 AC: 1118 AN: 2112

Alfa AF: 0.473 Hom.: 64776

Bravo AF: 0.465

Asia WGS AF: 0.509 AC: 1768 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	3.6
DANN	Benign	0.64
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs6657751; hg19: chr1-102469386;