6-73395696-A-C

Variant names:

• chr6-73395696-A-C
• rs17756426
• NM_018665.3:c.250+541A>C

Variant summary

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

The NM_018665.3(DDX43):​c.250+541A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0832 in 152,016 control chromosomes in the GnomAD database, including 598 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 0.083 (598 hom., cov: 31)
• Consequence: DDX43 NM_018665.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 2 publications found

Genes affected

DDX43 (HGNC:18677): (DEAD-box helicase 43) The protein encoded by this gene is an ATP-dependent RNA helicase in the DEAD-box family and displays tumor-specific expression. [provided by RefSeq, Jul 2008]

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 (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018665.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX43	NM_018665.3	MANE Select	c.250+541A>C		intron	N/A	NP_061135.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX43	ENST00000370336.5	TSL:1 MANE Select	c.250+541A>C		intron	N/A	ENSP00000359361.4
	DDX43	ENST00000464221.1	TSL:4	n.262+541A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0833 AC: 12650 AN: 151898 Hom.: 599 Cov.: 31

Gnomad AFR AF: 0.0460

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.0968

Gnomad EAS AF: 0.00962

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0975

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0832 AC: 12653 AN: 152016 Hom.: 598 Cov.: 31 AF XY: 0.0851 AC XY: 6326 AN XY: 74320

African (AFR) AF: 0.0460 AC: 1909 AN: 41490

American (AMR) AF: 0.0910 AC: 1388 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0968 AC: 336 AN: 3472

East Asian (EAS) AF: 0.00984 AC: 51 AN: 5184

South Asian (SAS) AF: 0.136 AC: 655 AN: 4820

European-Finnish (FIN) AF: 0.118 AC: 1240 AN: 10500

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0975 AC: 6627 AN: 67982

Other (OTH) AF: 0.0805 AC: 170 AN: 2112

Alfa AF: 0.0909 Hom.: 340

Bravo AF: 0.0784

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.64
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs17756426; hg19: chr6-74105419;