rs6768376

Variant names:

• chr3-59537812-G-A
• rs6768376
• ENST00000668131.1:n.372+815G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-59537812-G-A
• chr3-59537812-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668131.1(CFAP20DC-DT):​n.372+815G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 152,126 control chromosomes in the GnomAD database, including 382 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 0.058 (382 hom., cov: 32)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429
• Publications: 0 publications found

Genes affected

CFAP20DC-DT (HGNC:55618): (CFAP20DC divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668131.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP20DC-DT	ENST00000668131.1		n.372+815G>A		intron	N/A
	CFAP20DC-DT	ENST00000765324.1		n.238+815G>A		intron	N/A
	CFAP20DC-DT	ENST00000765325.1		n.294+815G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0577 AC: 8768 AN: 152008 Hom.: 378 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0501

Gnomad ASJ AF: 0.0377

Gnomad EAS AF: 0.00656

Gnomad SAS AF: 0.0258

Gnomad FIN AF: 0.0215

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0354

Gnomad OTH AF: 0.0484

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

GnomAD4 genome AF: 0.0578 AC: 8796 AN: 152126 Hom.: 382 Cov.: 32 AF XY: 0.0567 AC XY: 4213 AN XY: 74364

African (AFR) AF: 0.118 AC: 4915 AN: 41506

American (AMR) AF: 0.0501 AC: 765 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0377 AC: 131 AN: 3472

East Asian (EAS) AF: 0.00658 AC: 34 AN: 5170

South Asian (SAS) AF: 0.0260 AC: 125 AN: 4808

European-Finnish (FIN) AF: 0.0215 AC: 228 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0354 AC: 2405 AN: 67984

Other (OTH) AF: 0.0526 AC: 111 AN: 2110

Alfa AF: 0.0433 Hom.: 778

Bravo AF: 0.0643

Asia WGS AF: 0.0390 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.2
DANN	Benign	0.66
PhyloP100		0.43

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6768376;

hg19: chr3-59523538;