rs12721595

Variant names:

• chr8-6926488-T-C
• rs12721595
• ENST00000734108.1:n.367-308T>C

Variant summary

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

The ENST00000734108.1(ENSG00000295932):​n.367-308T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 152,220 control chromosomes in the GnomAD database, including 566 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 0.073 (566 hom., cov: 33)
• Consequence: ENSG00000295932 ENST00000734108.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 0 publications found

Genes affected

ENSG00000295932 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.222 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000734108.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295932	ENST00000734108.1		n.367-308T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 11058 AN: 152102 Hom.: 568 Cov.: 33

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0868

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.0883

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0632

Gnomad OTH AF: 0.0646

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

GnomAD4 genome AF: 0.0727 AC: 11064 AN: 152220 Hom.: 566 Cov.: 33 AF XY: 0.0794 AC XY: 5906 AN XY: 74416

African (AFR) AF: 0.0303 AC: 1259 AN: 41550

American (AMR) AF: 0.138 AC: 2117 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0868 AC: 301 AN: 3468

East Asian (EAS) AF: 0.233 AC: 1201 AN: 5160

South Asian (SAS) AF: 0.0881 AC: 425 AN: 4822

European-Finnish (FIN) AF: 0.117 AC: 1235 AN: 10600

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0632 AC: 4298 AN: 68014

Other (OTH) AF: 0.0630 AC: 133 AN: 2112

Alfa AF: 0.0650 Hom.: 215

Bravo AF: 0.0726

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.61
PhyloP100		-1.1
PromoterAI		0.00050	Neutral

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: rs12721595;

hg19: chr8-6784010;