rs1027242

chr3-167860439-A-Gchr3-167860439-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 0.57 in 151,994 control chromosomes in the GnomAD database, including 25,160 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 0.57 (25160 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.645 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: 0.570 AC: 86526 AN: 151876 Hom.: 25131 Cov.: 31

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.570 AC: 86615 AN: 151994 Hom.: 25160 Cov.: 31 AF XY: 0.567 AC XY: 42104 AN XY: 74308

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.588

Alfa AF: 0.551 Hom.: 52815

Bravo AF: 0.585

Asia WGS AF: 0.370 AC: 1286 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	0.13
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1027242; hg19: chr3-167578227;