1-65419886-G-C

Position:

• chr1-65419886-G-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 0.463 in 151,908 control chromosomes in the GnomAD database, including 16,798 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 0.46 (16798 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.705

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70375 AN: 151790 Hom.: 16793 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.463 AC: 70398 AN: 151908 Hom.: 16798 Cov.: 31 AF XY: 0.469 AC XY: 34809 AN XY: 74238

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.468

Alfa AF: 0.453 Hom.: 1920

Bravo AF: 0.458

Asia WGS AF: 0.631 AC: 2196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1327118; hg19: chr1-65885569; COSMIC: COSV60765595;