1-67682670-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 0.68 in 151,990 control chromosomes in the GnomAD database, including 36,799 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 0.68 (36799 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103371 AN: 151872 Hom.: 36804 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.680 AC: 103405 AN: 151990 Hom.: 36799 Cov.: 32 AF XY: 0.678 AC XY: 50352 AN XY: 74314

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.708

Alfa AF: 0.751 Hom.: 20836

Bravo AF: 0.667

Asia WGS AF: 0.614 AC: 2136 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	6.9
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs520820; hg19: chr1-68148353;