1-157723195-T-C

Variant names:

• chr1-157723195-T-C
• rs2210918

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 0.563 in 152,014 control chromosomes in the GnomAD database, including 26,243 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 0.56 (26243 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

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 = 0.828 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: 0.562 AC: 85418 AN: 151896 Hom.: 26195 Cov.: 31

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.563 AC: 85515 AN: 152014 Hom.: 26243 Cov.: 31 AF XY: 0.557 AC XY: 41369 AN XY: 74290

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.545

Alfa AF: 0.505 Hom.: 3598

Bravo AF: 0.581

Asia WGS AF: 0.515 AC: 1792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2210918; hg19: chr1-157692985;