chr6-129540247-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723409	XR_001743859.2	n.11605+200A>G		intron_variant	Intron 2 of 6
LOC102723409	XR_001743860.2	n.11605+200A>G		intron_variant	Intron 2 of 7
LOC102723409	XR_007059754.1	n.11605+200A>G		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226149	ENST00000419061.2	n.328+200A>G		intron_variant	Intron 2 of 4	3
ENSG00000226149	ENST00000430296.5	n.240+200A>G		intron_variant	Intron 3 of 6	5
ENSG00000226149	ENST00000657779.1	n.253+200A>G		intron_variant	Intron 3 of 9

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 v4.3

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

Other links and lift over

dbSNP: rs2275215; hg19: chr6-129861392;