rs718391

Variant names:

• chr1-25799343-C-G
• rs718391

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 0.549 in 152,074 control chromosomes in the GnomAD database, including 23,201 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 0.55 (23201 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.712 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: 0.549 AC: 83415 AN: 151956 Hom.: 23181 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.549 AC: 83473 AN: 152074 Hom.: 23201 Cov.: 32 AF XY: 0.553 AC XY: 41118 AN XY: 74352

African (AFR) AF: 0.498 AC: 20650 AN: 41496

American (AMR) AF: 0.640 AC: 9785 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1583 AN: 3470

East Asian (EAS) AF: 0.639 AC: 3306 AN: 5174

South Asian (SAS) AF: 0.732 AC: 3530 AN: 4824

European-Finnish (FIN) AF: 0.532 AC: 5642 AN: 10602

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37094 AN: 67912

Other (OTH) AF: 0.543 AC: 1146 AN: 2112

Alfa AF: 0.551 Hom.: 2889

Bravo AF: 0.547

Asia WGS AF: 0.694 AC: 2417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.3
DANN	Benign	0.76
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs718391; hg19: chr1-26125834;