rs2689178

Positions:

• chr1-238767053-T-C

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 0.673 in 152,026 control chromosomes in the GnomAD database, including 35,004 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 0.67 (35004 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102201 AN: 151908 Hom.: 34956 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.673 AC: 102312 AN: 152026 Hom.: 35004 Cov.: 32 AF XY: 0.667 AC XY: 49564 AN XY: 74316

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.669

Alfa AF: 0.658 Hom.: 14026

Bravo AF: 0.682

Asia WGS AF: 0.457 AC: 1586 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2689178; hg19: chr1-238930353;