chr7-97020572-A-AG

Position:

• chr7-97020572-A-AG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_005221.6(DLX5):​c.*163_*164insC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 662,438 control chromosomes in the GnomAD database, including 34,163 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.28 (6941 hom., cov: 23)
  • Exomes 𝑓: 0.31 (27222 hom.)
• Consequence: DLX5 NM_005221.6 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.13

Genes affected

DLX5 (HGNC:2918): (distal-less homeobox 5) This gene encodes a member of a homeobox transcription factor gene family similiar to the Drosophila distal-less gene. The encoded protein may play a role in bone development and fracture healing. Mutation in this gene, which is located in a tail-to-tail configuration with another member of the family on the long arm of chromosome 7, may be associated with split-hand/split-foot malformation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 7-97020572-A-AG is Benign according to our data. Variant chr7-97020572-A-AG is described in ClinVar as [Benign]. Clinvar id is 1257370.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLX5	NM_005221.6	c.*163_*164insC		3_prime_UTR_variant	3/3	ENST00000648378.1	NP_005212.1
DLX5	XM_005250185.4	c.*163_*164insC		3_prime_UTR_variant	3/3		XP_005250242.1
DLX5	XM_017011803.2	c.*163_*164insC		3_prime_UTR_variant	3/3		XP_016867292.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLX5	ENST00000648378.1	c.*163_*164insC		3_prime_UTR_variant	3/3		NM_005221.6	ENSP00000498116	P1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42224 AN: 151896 Hom.: 6951 Cov.: 23

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.294

GnomAD4 exome AF: 0.314 AC: 160038 AN: 510424 Hom.: 27222 Cov.: 8 AF XY: 0.315 AC XY: 80150 AN XY: 254064

Gnomad4 AFR exome AF: 0.0910

Gnomad4 AMR exome AF: 0.179

Gnomad4 ASJ exome AF: 0.334

Gnomad4 EAS exome AF: 0.269

Gnomad4 SAS exome AF: 0.327

Gnomad4 FIN exome AF: 0.412

Gnomad4 NFE exome AF: 0.322

Gnomad4 OTH exome AF: 0.303

GnomAD4 genome AF: 0.278 AC: 42212 AN: 152014 Hom.: 6941 Cov.: 23 AF XY: 0.283 AC XY: 21018 AN XY: 74272

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.294

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs3214218; hg19: chr7-96649884;