chr2-38874067-C-A

Variant names:

• chr2-38874067-C-A
• rs12479213
• NM_198963.3:c.-7+1720G>T

Variant summary

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

The NM_198963.3(DHX57):​c.-7+1720G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,784 control chromosomes in the GnomAD database, including 4,156 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 0.20 (4156 hom., cov: 31)
• Consequence: DHX57 NM_198963.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 7 publications found

Genes affected

DHX57 (HGNC:20086): (DExH-box helicase 57) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198963.3. 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
	DHX57	NM_198963.3	MANE Select	c.-7+1720G>T		intron	N/A	NP_945314.1
	DHX57	NM_001329963.1		c.-180+1720G>T		intron	N/A	NP_001316892.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DHX57	ENST00000457308.6	TSL:1 MANE Select	c.-7+1720G>T		intron	N/A	ENSP00000405111.2
	DHX57	ENST00000474104.5	TSL:1	n.93+1720G>T		intron	N/A
	DHX57	ENST00000622155.4	TSL:1	n.139+1720G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30399 AN: 151668 Hom.: 4159 Cov.: 31

Gnomad AFR AF: 0.0482

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.200 AC: 30397 AN: 151784 Hom.: 4156 Cov.: 31 AF XY: 0.207 AC XY: 15373 AN XY: 74178

African (AFR) AF: 0.0480 AC: 1990 AN: 41436

American (AMR) AF: 0.267 AC: 4063 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 712 AN: 3472

East Asian (EAS) AF: 0.570 AC: 2947 AN: 5166

South Asian (SAS) AF: 0.128 AC: 617 AN: 4802

European-Finnish (FIN) AF: 0.348 AC: 3661 AN: 10518

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15789 AN: 67890

Other (OTH) AF: 0.208 AC: 438 AN: 2104

Alfa AF: 0.204 Hom.: 3991

Bravo AF: 0.190

Asia WGS AF: 0.340 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		0.21
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: rs12479213; hg19: chr2-39101209;