3-423793-T-C

Variant names:

• chr3-423793-T-C
• rs6805861

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 0.871 in 152,168 control chromosomes in the GnomAD database, including 60,378 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 0.87 (60378 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 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: 0.871 AC: 132511 AN: 152050 Hom.: 60355 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.981

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.871 AC: 132579 AN: 152168 Hom.: 60378 Cov.: 32 AF XY: 0.874 AC XY: 65054 AN XY: 74402

African (AFR) AF: 0.573 AC: 23760 AN: 41456

American (AMR) AF: 0.930 AC: 14205 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3448 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5180 AN: 5182

South Asian (SAS) AF: 0.982 AC: 4735 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10613 AN: 10618

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67588 AN: 68034

Other (OTH) AF: 0.888 AC: 1876 AN: 2112

Alfa AF: 0.929 Hom.: 88507

Bravo AF: 0.852

Asia WGS AF: 0.960 AC: 3339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.40
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6805861; hg19: chr3-465476;