rs1910236

Variant names:

• chr3-59448694-G-A
• rs1910236
• ENST00000668131.1:n.307+87150G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-59448694-G-A
• chr3-59448694-G-C
• chr3-59448694-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.307+87150G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,048 control chromosomes in the GnomAD database, including 30,325 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 0.60 (30325 hom., cov: 32)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 9 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 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.307+87150G>A		intron	N/A
	CFAP20DC-DT	ENST00000765325.1		n.79+899G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91618 AN: 151930 Hom.: 30253 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.603 AC: 91748 AN: 152048 Hom.: 30325 Cov.: 32 AF XY: 0.603 AC XY: 44838 AN XY: 74324

African (AFR) AF: 0.867 AC: 35977 AN: 41506

American (AMR) AF: 0.604 AC: 9232 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1492 AN: 3472

East Asian (EAS) AF: 0.891 AC: 4600 AN: 5160

South Asian (SAS) AF: 0.489 AC: 2359 AN: 4822

European-Finnish (FIN) AF: 0.459 AC: 4841 AN: 10542

Middle Eastern (MID) AF: 0.517 AC: 150 AN: 290

European-Non Finnish (NFE) AF: 0.461 AC: 31315 AN: 67950

Other (OTH) AF: 0.596 AC: 1258 AN: 2110

Alfa AF: 0.512 Hom.: 67570

Bravo AF: 0.631

Asia WGS AF: 0.720 AC: 2505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.45
PhyloP100		-0.61

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: rs1910236;

hg19: chr3-59434420;