chr3-187600993-G-T

Position:

• chr3-187600993-G-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 0.344 in 152,068 control chromosomes in the GnomAD database, including 9,955 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 0.34 (9955 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52260 AN: 151950 Hom.: 9944 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.344 AC: 52291 AN: 152068 Hom.: 9955 Cov.: 32 AF XY: 0.348 AC XY: 25879 AN XY: 74322

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.335

Alfa AF: 0.375 Hom.: 1914

Bravo AF: 0.336

Asia WGS AF: 0.437 AC: 1522 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0040
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1376969; hg19: chr3-187318781;