chr1-65652146-A-C

Variant names:

• chr1-65652146-A-C
• rs1938492

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 0.437 in 151,752 control chromosomes in the GnomAD database, including 15,236 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 0.44 (15236 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.437 AC: 66256 AN: 151634 Hom.: 15198 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.437 AC: 66355 AN: 151752 Hom.: 15236 Cov.: 31 AF XY: 0.445 AC XY: 33044 AN XY: 74180

African (AFR) AF: 0.454 AC: 18756 AN: 41328

American (AMR) AF: 0.473 AC: 7214 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1295 AN: 3460

East Asian (EAS) AF: 0.870 AC: 4476 AN: 5146

South Asian (SAS) AF: 0.462 AC: 2221 AN: 4808

European-Finnish (FIN) AF: 0.492 AC: 5192 AN: 10544

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.382 AC: 25904 AN: 67898

Other (OTH) AF: 0.423 AC: 890 AN: 2106

Alfa AF: 0.409 Hom.: 19128

Bravo AF: 0.436

Asia WGS AF: 0.624 AC: 2168 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	2.3
DANN	Benign	0.45
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1938492; hg19: chr1-66117829; COSMIC: COSV59170817;