chr6-25099897-G-A

Position:

• chr6-25099897-G-A

Variant summary

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

The ENST00000377993.8(CMAHP):​n.1018-2696C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,120 control chromosomes in the GnomAD database, including 40,415 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 0.72 (40415 hom., cov: 32)
• Consequence: CMAHP ENST00000377993.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

Genes affected

CMAHP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CMAHP	NR_002174.2	n.1010-2696C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CMAHP	ENST00000377993.8	n.1018-2696C>T		intron_variant		1
CMAHP	ENST00000377989.8	n.1530-2696C>T		intron_variant		2
CMAHP	ENST00000490939.1	n.244-2696C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109190 AN: 152002 Hom.: 40396 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.718 AC: 109250 AN: 152120 Hom.: 40415 Cov.: 32 AF XY: 0.724 AC XY: 53810 AN XY: 74372

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.739

Alfa AF: 0.744 Hom.: 5327

Bravo AF: 0.705

Asia WGS AF: 0.828 AC: 2879 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.31
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3792970; hg19: chr6-25100125;