chr1-102648125-T-C

Position:

• chr1-102648125-T-C

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 0.497 in 151,996 control chromosomes in the GnomAD database, including 20,854 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 0.50 (20854 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.102648125T>C		intergenic_region
LOC105378874	XR_947651.2	n.159-100A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75483 AN: 151878 Hom.: 20838 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.497 AC: 75511 AN: 151996 Hom.: 20854 Cov.: 32 AF XY: 0.506 AC XY: 37548 AN XY: 74274

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.501

Alfa AF: 0.408 Hom.: 1274

Bravo AF: 0.483

Asia WGS AF: 0.582 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs977155; hg19: chr1-103113681;