3-98066703-T-C

Variant names:

• chr3-98066703-T-C
• rs6439591

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 151,716 control chromosomes in the GnomAD database, including 24,280 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 (24280 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

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 (AFR) allele frequency at 95% confidence interval = 0.612 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: 85264 AN: 151598 Hom.: 24250 Cov.: 31

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.563 AC: 85354 AN: 151716 Hom.: 24280 Cov.: 31 AF XY: 0.559 AC XY: 41434 AN XY: 74116

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.577

Alfa AF: 0.538 Hom.: 9880

Bravo AF: 0.566

Asia WGS AF: 0.492 AC: 1713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6439591; hg19: chr3-97785547;