rs4660275

Variant names:

• chr1-44379286-G-A
• rs4660275

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 0.253 in 152,148 control chromosomes in the GnomAD database, including 4,893 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 0.25 (4893 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 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: 0.253 AC: 38440 AN: 152030 Hom.: 4894 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.253 AC: 38453 AN: 152148 Hom.: 4893 Cov.: 32 AF XY: 0.252 AC XY: 18732 AN XY: 74390

African (AFR) AF: 0.252 AC: 10439 AN: 41500

American (AMR) AF: 0.252 AC: 3860 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 803 AN: 3472

East Asian (EAS) AF: 0.188 AC: 975 AN: 5176

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4820

European-Finnish (FIN) AF: 0.237 AC: 2509 AN: 10604

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17939 AN: 67980

Other (OTH) AF: 0.267 AC: 564 AN: 2110

Alfa AF: 0.262 Hom.: 22951

Bravo AF: 0.255

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.56
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs4660275; hg19: chr1-44844958;