chr3-98066703-T-C

Variant names:

• chr3-98066703-T-C
• rs6439591

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.619 AC: 25607 AN: 41394

American (AMR) AF: 0.534 AC: 8122 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3466

East Asian (EAS) AF: 0.372 AC: 1910 AN: 5132

South Asian (SAS) AF: 0.555 AC: 2672 AN: 4816

European-Finnish (FIN) AF: 0.500 AC: 5276 AN: 10552

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38056 AN: 67816

Other (OTH) AF: 0.577 AC: 1220 AN: 2114

Alfa AF: 0.543 Hom.: 11310

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
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs6439591; hg19: chr3-97785547;