rs12202969

Variant names:

• chr6-98128347-G-A
• rs12202969
• ENST00000606913.5:n.240+29077G>A

Variant summary

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

The ENST00000607032.1(ENSG00000271860):​n.410+29077G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,914 control chromosomes in the GnomAD database, including 12,405 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 0.39 (12405 hom., cov: 31)
• Consequence: ENSG00000271860 ENST00000607032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 23 publications found

Genes affected

ENSG00000271860 (HGNC:58964):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607032.1. 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
	ENSG00000271860	ENST00000606913.5	TSL:5	n.240+29077G>A		intron	N/A
	ENSG00000271860	ENST00000607032.1	TSL:3	n.410+29077G>A		intron	N/A
	ENSG00000271860	ENST00000607823.5	TSL:5	n.352+29077G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58723 AN: 151796 Hom.: 12409 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.387 AC: 58716 AN: 151914 Hom.: 12405 Cov.: 31 AF XY: 0.384 AC XY: 28540 AN XY: 74236

African (AFR) AF: 0.219 AC: 9077 AN: 41450

American (AMR) AF: 0.346 AC: 5272 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1670 AN: 3472

East Asian (EAS) AF: 0.398 AC: 2055 AN: 5168

South Asian (SAS) AF: 0.268 AC: 1291 AN: 4812

European-Finnish (FIN) AF: 0.491 AC: 5166 AN: 10530

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32806 AN: 67930

Other (OTH) AF: 0.390 AC: 822 AN: 2106

Alfa AF: 0.455 Hom.: 22139

Bravo AF: 0.371

Asia WGS AF: 0.268 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.27
PhyloP100		-0.35

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: rs12202969;

hg19: chr6-98576223;