rs6438101

Variant names:

• chr3-112734282-G-A
• rs6438101

Your query was ambiguous. Multiple possible variants found:

• chr3-112734282-G-A
• chr3-112734282-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 0.449 in 152,060 control chromosomes in the GnomAD database, including 16,405 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 0.45 (16405 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.53 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: 0.449 AC: 68199 AN: 151942 Hom.: 16395 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.449 AC: 68242 AN: 152060 Hom.: 16405 Cov.: 31 AF XY: 0.450 AC XY: 33434 AN XY: 74304

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.434

Alfa AF: 0.507 Hom.: 40490

Bravo AF: 0.436

Asia WGS AF: 0.422 AC: 1464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6438101; hg19: chr3-112453129;