1-67671380-C-T

Position:

• chr1-67671380-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 0.406 in 151,954 control chromosomes in the GnomAD database, including 14,730 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 0.41 (14730 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.67671380C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61690 AN: 151836 Hom.: 14728 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.406 AC: 61688 AN: 151954 Hom.: 14730 Cov.: 31 AF XY: 0.404 AC XY: 29995 AN XY: 74286

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.443

Alfa AF: 0.462 Hom.: 3007

Bravo AF: 0.395

Asia WGS AF: 0.415 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.95
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1408956; hg19: chr1-68137063;