rs12202969

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000271860 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271860	ENST00000606913.5	n.240+29077G>A		intron_variant	Intron 2 of 4	5
ENSG00000271860	ENST00000607032.1	n.410+29077G>A		intron_variant	Intron 4 of 7	3
ENSG00000271860	ENST00000607823.5	n.352+29077G>A		intron_variant	Intron 4 of 6	5

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

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.390

Alfa AF: 0.421 Hom.: 1739

Bravo AF: 0.371

Asia WGS AF: 0.268 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12202969; hg19: chr6-98576223;