rs4648310

Variant names:

• chr1-186671393-T-C
• rs4648310

Your query was ambiguous. Multiple possible variants found:

• chr1-186671393-T-C
• chr1-186671393-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0227 in 152,252 control chromosomes in the GnomAD database, including 57 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 0.023 (57 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0227 (3456/152252) while in subpopulation NFE AF = 0.0334 (2271/67992). AF 95% confidence interval is 0.0323. There are 57 homozygotes in GnomAd4. There are 1706 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 57 gene

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: 0.0227 AC: 3456 AN: 152134 Hom.: 57 Cov.: 32

Gnomad AFR AF: 0.00562

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.0482

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0230

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

GnomAD4 genome AF: 0.0227 AC: 3456 AN: 152252 Hom.: 57 Cov.: 32 AF XY: 0.0229 AC XY: 1706 AN XY: 74446

African (AFR) AF: 0.00561 AC: 233 AN: 41560

American (AMR) AF: 0.0227 AC: 347 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00923 AC: 32 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00187 AC: 9 AN: 4822

European-Finnish (FIN) AF: 0.0482 AC: 512 AN: 10628

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0334 AC: 2271 AN: 67992

Other (OTH) AF: 0.0227 AC: 48 AN: 2112

Alfa AF: 0.0166 Hom.: 10

Bravo AF: 0.0194

Asia WGS AF: 0.00404 AC: 14 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.19
DANN	Benign	0.52
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs4648310; hg19: chr1-186640525;