rs12197043

Variant names:

• chr6-149130141-A-G
• rs12197043
• ENST00000834740.1:n.228+38784T>C

Variant summary

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

The ENST00000834740.1(ENSG00000308521):​n.228+38784T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,066 control chromosomes in the GnomAD database, including 10,384 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 0.37 (10384 hom., cov: 32)
• Consequence: ENSG00000308521 ENST00000834740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 3 publications found

Genes affected

ENSG00000308521 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834740.1. 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
	ENSG00000308521	ENST00000834740.1		n.228+38784T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55693 AN: 151948 Hom.: 10384 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.367 AC: 55734 AN: 152066 Hom.: 10384 Cov.: 32 AF XY: 0.366 AC XY: 27182 AN XY: 74322

African (AFR) AF: 0.379 AC: 15710 AN: 41466

American (AMR) AF: 0.381 AC: 5820 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1702 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1105 AN: 5178

South Asian (SAS) AF: 0.315 AC: 1524 AN: 4832

European-Finnish (FIN) AF: 0.365 AC: 3849 AN: 10548

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24814 AN: 67966

Other (OTH) AF: 0.403 AC: 851 AN: 2114

Alfa AF: 0.361 Hom.: 1260

Bravo AF: 0.372

Asia WGS AF: 0.298 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.55
DANN	Benign	0.76
PhyloP100		-1.6

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: rs12197043;

hg19: chr6-149451277;