rs9356970

Variant names:

• chr6-25257738-G-A
• rs9356970
• ENST00000413898.3:n.519-2432C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-25257738-G-A
• chr6-25257738-G-C
• chr6-25257738-G-T

Variant summary

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

The ENST00000413898.3(CMAHP):​n.519-2432C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,202 control chromosomes in the GnomAD database, including 7,886 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 0.29 (7886 hom., cov: 33)
• Consequence: CMAHP ENST00000413898.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 1 publications found

Genes affected

CMAHP (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413898.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101928663	NR_110862.1		n.514-2432C>T		intron	N/A
	LOC101928663	NR_110863.1		n.513+2610C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMAHP	ENST00000413898.3	TSL:1	n.519-2432C>T		intron	N/A
	CMAHP	ENST00000643481.1		n.517-2432C>T		intron	N/A
	CMAHP	ENST00000643656.2		n.267-2432C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43473 AN: 152086 Hom.: 7882 Cov.: 33

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.286 AC: 43477 AN: 152202 Hom.: 7886 Cov.: 33 AF XY: 0.298 AC XY: 22158 AN XY: 74412

African (AFR) AF: 0.0715 AC: 2970 AN: 41554

American (AMR) AF: 0.332 AC: 5070 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3176 AN: 5174

South Asian (SAS) AF: 0.460 AC: 2218 AN: 4826

European-Finnish (FIN) AF: 0.454 AC: 4807 AN: 10582

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23100 AN: 67986

Other (OTH) AF: 0.264 AC: 559 AN: 2114

Alfa AF: 0.300 Hom.: 9612

Bravo AF: 0.262

Asia WGS AF: 0.467 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.75
PhyloP100		-0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9356970;

hg19: chr6-25257966;