rs1416156

chr1-218224238-A-Gchr1-218224238-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 0.655 in 152,050 control chromosomes in the GnomAD database, including 33,271 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 0.66 (33271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 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: 0.655 AC: 99531 AN: 151932 Hom.: 33210 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.655 AC: 99649 AN: 152050 Hom.: 33271 Cov.: 32 AF XY: 0.659 AC XY: 48948 AN XY: 74286

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.678

Alfa AF: 0.608 Hom.: 57403

Bravo AF: 0.676

Asia WGS AF: 0.809 AC: 2812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1416156; hg19: chr1-218397580; COSMIC: COSV60027916;