1-223108398-T-C

Variant names:

• chr1-223108398-T-C
• rs4661282

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 0.339 in 152,130 control chromosomes in the GnomAD database, including 10,110 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 0.34 (10110 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.747
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 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: 0.339 AC: 51573 AN: 152012 Hom.: 10109 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.339 AC: 51601 AN: 152130 Hom.: 10110 Cov.: 32 AF XY: 0.342 AC XY: 25416 AN XY: 74364

African (AFR) AF: 0.146 AC: 6042 AN: 41512

American (AMR) AF: 0.325 AC: 4965 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1393 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1078 AN: 5176

South Asian (SAS) AF: 0.426 AC: 2047 AN: 4810

European-Finnish (FIN) AF: 0.501 AC: 5293 AN: 10570

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.434 AC: 29496 AN: 67988

Other (OTH) AF: 0.340 AC: 718 AN: 2114

Alfa AF: 0.385 Hom.: 1502

Bravo AF: 0.313

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.6
DANN	Benign	0.69
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs4661282; hg19: chr1-223281740;