1-47449561-A-T

Variant names:

• chr1-47449561-A-T
• rs564914

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 0.439 in 151,910 control chromosomes in the GnomAD database, including 15,306 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 0.44 (15306 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82
• Publications: 11 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 (AFR) allele frequency at 95% confidence interval = 0.576 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: 0.439 AC: 66581 AN: 151792 Hom.: 15292 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.439 AC: 66633 AN: 151910 Hom.: 15306 Cov.: 31 AF XY: 0.429 AC XY: 31884 AN XY: 74242

African (AFR) AF: 0.582 AC: 24117 AN: 41404

American (AMR) AF: 0.423 AC: 6467 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3464

East Asian (EAS) AF: 0.413 AC: 2116 AN: 5126

South Asian (SAS) AF: 0.283 AC: 1360 AN: 4808

European-Finnish (FIN) AF: 0.295 AC: 3117 AN: 10568

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26989 AN: 67948

Other (OTH) AF: 0.414 AC: 873 AN: 2108

Alfa AF: 0.237 Hom.: 478

Bravo AF: 0.458

Asia WGS AF: 0.332 AC: 1156 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	0.10
DANN	Benign	0.45
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs564914; hg19: chr1-47915233;