chr1-27931466-T-C

Variant names:

• chr1-27931466-T-C
• rs17257294

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 0.211 in 151,826 control chromosomes in the GnomAD database, including 3,908 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 0.21 (3908 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 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: 0.211 AC: 31960 AN: 151706 Hom.: 3897 Cov.: 30

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.211 AC: 31988 AN: 151826 Hom.: 3908 Cov.: 30 AF XY: 0.208 AC XY: 15437 AN XY: 74182

African (AFR) AF: 0.0881 AC: 3651 AN: 41438

American (AMR) AF: 0.266 AC: 4055 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3470

East Asian (EAS) AF: 0.245 AC: 1260 AN: 5136

South Asian (SAS) AF: 0.154 AC: 744 AN: 4816

European-Finnish (FIN) AF: 0.231 AC: 2438 AN: 10546

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18615 AN: 67886

Other (OTH) AF: 0.218 AC: 460 AN: 2110

Alfa AF: 0.242 Hom.: 617

Bravo AF: 0.207

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.84
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs17257294; hg19: chr1-28257977; COSMIC: COSV65870265;