rs10006706

Variant names:

• chr4-119487997-T-C
• rs10006706
• ENST00000502760.2:n.772-5336T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-119487997-T-C
• chr4-119487997-T-G

Variant summary

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

The ENST00000502760.2(ENSG00000291203):​n.772-5336T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,962 control chromosomes in the GnomAD database, including 5,470 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 0.27 (5470 hom., cov: 32)
• Consequence: ENSG00000291203 ENST00000502760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738
• Publications: 4 publications found

Genes affected

ENSG00000291203 (HGNC:):

SEPTIN7P14 (HGNC:44219): (septin 7 pseudogene 14)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502760.2. 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
	SEPTIN7P14	NR_037630.1		n.728-5336T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291203	ENST00000502760.2	TSL:3	n.772-5336T>C		intron	N/A
	ENSG00000291203	ENST00000508519.6	TSL:3	n.663-648T>C		intron	N/A
	ENSG00000291203	ENST00000510011.6	TSL:3	n.661-5336T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40318 AN: 151844 Hom.: 5466 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.266 AC: 40351 AN: 151962 Hom.: 5470 Cov.: 32 AF XY: 0.263 AC XY: 19562 AN XY: 74256

African (AFR) AF: 0.227 AC: 9410 AN: 41496

American (AMR) AF: 0.264 AC: 4019 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1951 AN: 5118

South Asian (SAS) AF: 0.176 AC: 852 AN: 4830

European-Finnish (FIN) AF: 0.253 AC: 2681 AN: 10580

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19882 AN: 67920

Other (OTH) AF: 0.278 AC: 588 AN: 2112

Alfa AF: 0.186 Hom.: 542

Bravo AF: 0.271

Asia WGS AF: 0.251 AC: 871 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-0.74

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: rs10006706;

hg19: chr4-120409152;