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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0477 AC: 1979 AN: 41530

American (AMR) AF: 0.348 AC: 5316 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 688 AN: 3466

East Asian (EAS) AF: 0.628 AC: 3235 AN: 5152

South Asian (SAS) AF: 0.392 AC: 1886 AN: 4816

European-Finnish (FIN) AF: 0.223 AC: 2356 AN: 10576

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16707 AN: 67976

Other (OTH) AF: 0.219 AC: 464 AN: 2116

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
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1338625; hg19: chr1-164514265;