rs223248

Variant names:

• chr1-96085773-G-T
• rs223248

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 0.427 in 152,008 control chromosomes in the GnomAD database, including 14,842 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 0.43 (14842 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 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: 0.427 AC: 64925 AN: 151892 Hom.: 14842 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.427 AC: 64938 AN: 152008 Hom.: 14842 Cov.: 32 AF XY: 0.428 AC XY: 31803 AN XY: 74304

African (AFR) AF: 0.300 AC: 12423 AN: 41452

American (AMR) AF: 0.400 AC: 6105 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1547 AN: 3462

East Asian (EAS) AF: 0.102 AC: 529 AN: 5178

South Asian (SAS) AF: 0.478 AC: 2302 AN: 4814

European-Finnish (FIN) AF: 0.580 AC: 6126 AN: 10554

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34308 AN: 67960

Other (OTH) AF: 0.441 AC: 932 AN: 2114

Alfa AF: 0.486 Hom.: 9311

Bravo AF: 0.407

Asia WGS AF: 0.281 AC: 979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.35
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs223248; hg19: chr1-96551329;