chr1-102635356-C-T

Position:

• chr1-102635356-C-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 0.472 in 151,906 control chromosomes in the GnomAD database, including 20,016 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 0.47 (20016 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.102635356C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71676 AN: 151788 Hom.: 20002 Cov.: 31

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.472 AC: 71693 AN: 151906 Hom.: 20016 Cov.: 31 AF XY: 0.481 AC XY: 35720 AN XY: 74216

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.484

Alfa AF: 0.514 Hom.: 2727

Bravo AF: 0.455

Asia WGS AF: 0.566 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.85
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1517432; hg19: chr1-103100912;