chr1-244227262-C-T

Variant names:

• chr1-244227262-C-T
• rs10429924

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 0.0944 in 152,028 control chromosomes in the GnomAD database, including 1,114 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 0.094 (1114 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 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: 0.0945 AC: 14351 AN: 151912 Hom.: 1113 Cov.: 31

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.0729

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0754

Gnomad OTH AF: 0.0892

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

GnomAD4 genome AF: 0.0944 AC: 14352 AN: 152028 Hom.: 1114 Cov.: 31 AF XY: 0.104 AC XY: 7688 AN XY: 74270

African (AFR) AF: 0.0389 AC: 1616 AN: 41496

American (AMR) AF: 0.160 AC: 2445 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0729 AC: 253 AN: 3472

East Asian (EAS) AF: 0.392 AC: 2016 AN: 5144

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4818

European-Finnish (FIN) AF: 0.151 AC: 1590 AN: 10534

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0754 AC: 5123 AN: 67988

Other (OTH) AF: 0.0954 AC: 201 AN: 2108

Alfa AF: 0.0833 Hom.: 1547

Bravo AF: 0.0966

Asia WGS AF: 0.255 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.40
DANN	Benign	0.66
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10429924; hg19: chr1-244390564;