rs1002539

Positions:

• chr6-25091112-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000377993.8(CMAHP):​n.1450+784T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,130 control chromosomes in the GnomAD database, including 5,094 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 0.26 (5094 hom., cov: 32)
• Consequence: CMAHP ENST00000377993.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

Genes affected

CMAHP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CMAHP	NR_002174.2	n.1442+784T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CMAHP	ENST00000377993.8	n.1450+784T>C		intron_variant		1
CMAHP	ENST00000377989.8	n.1962+784T>C		intron_variant		2
CMAHP	ENST00000490939.1	n.676+784T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38999 AN: 152012 Hom.: 5087 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.257 AC: 39023 AN: 152130 Hom.: 5094 Cov.: 32 AF XY: 0.255 AC XY: 18948 AN XY: 74368

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.249

Alfa AF: 0.258 Hom.: 640

Bravo AF: 0.258

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1002539; hg19: chr6-25091340;