1-52601914-T-C

Variant names:

• chr1-52601914-T-C
• rs6588431

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 0.618 in 152,058 control chromosomes in the GnomAD database, including 28,988 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 0.62 (28988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 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: 0.618 AC: 93868 AN: 151940 Hom.: 28975 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.618 AC: 93920 AN: 152058 Hom.: 28988 Cov.: 32 AF XY: 0.621 AC XY: 46173 AN XY: 74302

African (AFR) AF: 0.593 AC: 24599 AN: 41480

American (AMR) AF: 0.669 AC: 10215 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2220 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4107 AN: 5166

South Asian (SAS) AF: 0.691 AC: 3325 AN: 4814

European-Finnish (FIN) AF: 0.613 AC: 6472 AN: 10566

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40987 AN: 67974

Other (OTH) AF: 0.623 AC: 1314 AN: 2110

Alfa AF: 0.610 Hom.: 17128

Bravo AF: 0.621

Asia WGS AF: 0.764 AC: 2657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.72
PhyloP100		-0.66
PromoterAI		0.063	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6588431; hg19: chr1-53067586;