rs271738

Variant names:

• chr1-234527144-G-A
• rs271738

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.529 in 152,068 control chromosomes in the GnomAD database, including 23,292 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 0.53 (23292 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 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: 0.529 AC: 80333 AN: 151950 Hom.: 23256 Cov.: 33

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.529 AC: 80429 AN: 152068 Hom.: 23292 Cov.: 33 AF XY: 0.538 AC XY: 40004 AN XY: 74320

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.528

Alfa AF: 0.495 Hom.: 6245

Bravo AF: 0.551

Asia WGS AF: 0.840 AC: 2914 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	16
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs271738; hg19: chr1-234662890;