6-129540247-T-C

Variant names:

• chr6-129540247-T-C
• rs2275215
• ENST00000419061.2:n.328+200A>G

Variant summary

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

The ENST00000419061.2(ENSG00000226149):​n.328+200A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,016 control chromosomes in the GnomAD database, including 10,147 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 0.35 (10147 hom., cov: 32)
• Consequence: ENSG00000226149 ENST00000419061.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20
• Publications: 17 publications found

Genes affected

ENSG00000226149 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419061.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226149	ENST00000419061.2	TSL:3	n.328+200A>G		intron	N/A
	ENSG00000226149	ENST00000430296.5	TSL:5	n.240+200A>G		intron	N/A
	ENSG00000226149	ENST00000657779.1		n.253+200A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53274 AN: 151896 Hom.: 10144 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.351 AC: 53306 AN: 152016 Hom.: 10147 Cov.: 32 AF XY: 0.353 AC XY: 26231 AN XY: 74306

African (AFR) AF: 0.509 AC: 21080 AN: 41450

American (AMR) AF: 0.286 AC: 4372 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3462

East Asian (EAS) AF: 0.393 AC: 2028 AN: 5162

South Asian (SAS) AF: 0.452 AC: 2180 AN: 4820

European-Finnish (FIN) AF: 0.313 AC: 3301 AN: 10558

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18606 AN: 67970

Other (OTH) AF: 0.326 AC: 688 AN: 2110

Alfa AF: 0.292 Hom.: 22625

Bravo AF: 0.349

Asia WGS AF: 0.458 AC: 1591 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0010
DANN	Benign	0.26
PhyloP100		-3.2

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: rs2275215;

hg19: chr6-129861392;