chr1-65719720-G-A

Position:

• chr1-65719720-G-A

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 0.257 in 152,146 control chromosomes in the GnomAD database, including 5,439 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 0.26 (5439 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.309 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: 0.257 AC: 39128 AN: 152028 Hom.: 5440 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0237

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.257 AC: 39143 AN: 152146 Hom.: 5439 Cov.: 31 AF XY: 0.253 AC XY: 18836 AN XY: 74372

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.0237

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.263

Alfa AF: 0.298 Hom.: 14119

Bravo AF: 0.256

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7539471; hg19: chr1-66185403;