rs1327872

Variant names:

• chr1-190564570-G-A
• rs1327872

Your query was ambiguous. Multiple possible variants found:

• chr1-190564570-G-A
• chr1-190564570-G-C
• chr1-190564570-G-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 0.134 in 152,022 control chromosomes in the GnomAD database, including 1,568 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 0.13 (1568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.186 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: 0.134 AC: 20300 AN: 151904 Hom.: 1557 Cov.: 32

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0965

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.134 AC: 20324 AN: 152022 Hom.: 1568 Cov.: 32 AF XY: 0.135 AC XY: 10054 AN XY: 74272

African (AFR) AF: 0.0672 AC: 2788 AN: 41492

American (AMR) AF: 0.191 AC: 2920 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 360 AN: 3470

East Asian (EAS) AF: 0.169 AC: 868 AN: 5138

South Asian (SAS) AF: 0.0961 AC: 464 AN: 4826

European-Finnish (FIN) AF: 0.186 AC: 1966 AN: 10544

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10431 AN: 67990

Other (OTH) AF: 0.131 AC: 276 AN: 2108

Alfa AF: 0.146 Hom.: 5670

Bravo AF: 0.136

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.45
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1327872; hg19: chr1-190533700;