chr1-229428370-T-C

Variant names:

• chr1-229428370-T-C
• rs728614

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 0.703 in 152,066 control chromosomes in the GnomAD database, including 39,595 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 0.70 (39595 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 7 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 (EAS) allele frequency at 95% confidence interval = 0.825 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: 0.703 AC: 106796 AN: 151948 Hom.: 39583 Cov.: 31

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.703 AC: 106832 AN: 152066 Hom.: 39595 Cov.: 31 AF XY: 0.706 AC XY: 52449 AN XY: 74330

African (AFR) AF: 0.452 AC: 18727 AN: 41440

American (AMR) AF: 0.711 AC: 10859 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2207 AN: 3466

East Asian (EAS) AF: 0.846 AC: 4373 AN: 5172

South Asian (SAS) AF: 0.795 AC: 3823 AN: 4808

European-Finnish (FIN) AF: 0.857 AC: 9070 AN: 10586

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55345 AN: 68002

Other (OTH) AF: 0.696 AC: 1471 AN: 2112

Alfa AF: 0.773 Hom.: 190592

Bravo AF: 0.678

Asia WGS AF: 0.779 AC: 2711 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	0.66
DANN	Benign	0.50
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs728614; hg19: chr1-229564117;