rs1338625

Variant names:

• chr1-164545028-A-C
• rs1338625

Your query was ambiguous. Multiple possible variants found:

• chr1-164545028-A-C
• chr1-164545028-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.217 in 152,110 control chromosomes in the GnomAD database, including 4,887 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 0.22 (4887 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 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: 0.217 AC: 32930 AN: 151994 Hom.: 4879 Cov.: 31

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.217 AC: 32947 AN: 152110 Hom.: 4887 Cov.: 31 AF XY: 0.224 AC XY: 16671 AN XY: 74370

Gnomad4 AFR AF: 0.0477

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.219

Alfa AF: 0.245 Hom.: 897

Bravo AF: 0.220

Asia WGS AF: 0.449 AC: 1557 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1338625; hg19: chr1-164514265;