6-11930254-C-T

Variant names:

• chr6-11930254-C-T
• rs9380643
• ENST00000848130.1:n.334-21281C>T

Variant summary

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

The ENST00000848130.1(ENSG00000310201):​n.334-21281C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,004 control chromosomes in the GnomAD database, including 18,772 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 0.42 (18772 hom., cov: 32)
• Consequence: ENSG00000310201 ENST00000848130.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 1 publications found

Genes affected

ENSG00000310201 (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 = 0.826 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
ENSG00000310201	ENST00000848130.1	n.334-21281C>T		intron_variant	Intron 1 of 2
ENSG00000310201	ENST00000848131.1	n.238-21281C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64185 AN: 151884 Hom.: 18705 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.423 AC: 64316 AN: 152004 Hom.: 18772 Cov.: 32 AF XY: 0.423 AC XY: 31407 AN XY: 74300

African (AFR) AF: 0.834 AC: 34563 AN: 41464

American (AMR) AF: 0.346 AC: 5282 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1722 AN: 5166

South Asian (SAS) AF: 0.422 AC: 2031 AN: 4816

European-Finnish (FIN) AF: 0.247 AC: 2595 AN: 10518

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15884 AN: 67982

Other (OTH) AF: 0.429 AC: 905 AN: 2110

Alfa AF: 0.288 Hom.: 13299

Bravo AF: 0.447

Asia WGS AF: 0.410 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.57
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs9380643; hg19: chr6-11930487;