1-65419886-G-C

Variant names:

• chr1-65419886-G-C
• rs1327118

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 26 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.411 AC: 17038 AN: 41406

American (AMR) AF: 0.461 AC: 7046 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1540 AN: 3472

East Asian (EAS) AF: 0.856 AC: 4405 AN: 5144

South Asian (SAS) AF: 0.576 AC: 2780 AN: 4824

European-Finnish (FIN) AF: 0.475 AC: 5008 AN: 10546

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31025 AN: 67926

Other (OTH) AF: 0.468 AC: 985 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.46
PhyloP100		0.70

Splicing

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

Other links and lift over

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