rs4648308

Variant names:

• chr1-186671485-C-T
• rs4648308

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 0.262 in 152,046 control chromosomes in the GnomAD database, including 7,883 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 0.26 (7883 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 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: 0.262 AC: 39810 AN: 151928 Hom.: 7840 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0483

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.0821

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.262 AC: 39911 AN: 152046 Hom.: 7883 Cov.: 32 AF XY: 0.255 AC XY: 18977 AN XY: 74324

African (AFR) AF: 0.556 AC: 23043 AN: 41454

American (AMR) AF: 0.197 AC: 3002 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 807 AN: 3472

East Asian (EAS) AF: 0.0481 AC: 249 AN: 5180

South Asian (SAS) AF: 0.193 AC: 933 AN: 4830

European-Finnish (FIN) AF: 0.0821 AC: 869 AN: 10586

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10321 AN: 67928

Other (OTH) AF: 0.259 AC: 547 AN: 2116

Alfa AF: 0.225 Hom.: 886

Bravo AF: 0.283

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.15
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4648308; hg19: chr1-186640617;