chr1-65695778-T-C

Variant names:

• chr1-65695778-T-C
• rs4420065

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 0.572 in 152,026 control chromosomes in the GnomAD database, including 25,597 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 0.57 (25597 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86920 AN: 151908 Hom.: 25597 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.572 AC: 86943 AN: 152026 Hom.: 25597 Cov.: 33 AF XY: 0.562 AC XY: 41799 AN XY: 74336

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.579

Alfa AF: 0.601 Hom.: 53006

Bravo AF: 0.575

Asia WGS AF: 0.378 AC: 1318 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4420065; hg19: chr1-66161461;