1-226356719-T-C

Variant names:

• chr1-226356719-T-C
• rs12567614

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 0.495 in 151,998 control chromosomes in the GnomAD database, including 19,644 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 0.50 (19644 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 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: 0.495 AC: 75238 AN: 151880 Hom.: 19650 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.495 AC: 75256 AN: 151998 Hom.: 19644 Cov.: 32 AF XY: 0.490 AC XY: 36387 AN XY: 74284

African (AFR) AF: 0.378 AC: 15665 AN: 41422

American (AMR) AF: 0.484 AC: 7386 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2245 AN: 3468

East Asian (EAS) AF: 0.144 AC: 744 AN: 5170

South Asian (SAS) AF: 0.542 AC: 2609 AN: 4810

European-Finnish (FIN) AF: 0.486 AC: 5140 AN: 10570

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.583 AC: 39594 AN: 67972

Other (OTH) AF: 0.526 AC: 1108 AN: 2106

Alfa AF: 0.553 Hom.: 99558

Bravo AF: 0.486

Asia WGS AF: 0.386 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.34
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs12567614; hg19: chr1-226544420; COSMIC: COSV64691951;