1-233723005-A-G

Variant names:

• chr1-233723005-A-G
• rs963666

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 0.246 in 151,960 control chromosomes in the GnomAD database, including 5,643 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 0.25 (5643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 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: 0.246 AC: 37326 AN: 151838 Hom.: 5644 Cov.: 32

Gnomad AFR AF: 0.0600

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.246 AC: 37330 AN: 151960 Hom.: 5643 Cov.: 32 AF XY: 0.249 AC XY: 18467 AN XY: 74256

African (AFR) AF: 0.0601 AC: 2495 AN: 41518

American (AMR) AF: 0.341 AC: 5201 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1241 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1762 AN: 5116

South Asian (SAS) AF: 0.346 AC: 1661 AN: 4806

European-Finnish (FIN) AF: 0.261 AC: 2746 AN: 10528

Middle Eastern (MID) AF: 0.328 AC: 95 AN: 290

European-Non Finnish (NFE) AF: 0.311 AC: 21125 AN: 67952

Other (OTH) AF: 0.296 AC: 624 AN: 2110

Alfa AF: 0.293 Hom.: 22747

Bravo AF: 0.241

Asia WGS AF: 0.324 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.78
DANN	Benign	0.58
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs963666; hg19: chr1-233858751; COSMIC: COSV60040072;