6-91454381-C-T

Variant names:

• chr6-91454381-C-T
• rs4321804
• ENST00000721215.1:n.186-11416C>T

Variant summary

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

The ENST00000721215.1(ENSG00000294116):​n.186-11416C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,872 control chromosomes in the GnomAD database, including 22,665 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 0.54 (22665 hom., cov: 32)
• Consequence: ENSG00000294116 ENST00000721215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 2 publications found

Genes affected

ENSG00000294116 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 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
ENSG00000294116	ENST00000721215.1	n.186-11416C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81879 AN: 151754 Hom.: 22623 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.540 AC: 81968 AN: 151872 Hom.: 22665 Cov.: 32 AF XY: 0.542 AC XY: 40195 AN XY: 74214

African (AFR) AF: 0.655 AC: 27139 AN: 41438

American (AMR) AF: 0.555 AC: 8464 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2044 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2811 AN: 5154

South Asian (SAS) AF: 0.429 AC: 2068 AN: 4824

European-Finnish (FIN) AF: 0.530 AC: 5589 AN: 10542

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32282 AN: 67872

Other (OTH) AF: 0.517 AC: 1091 AN: 2112

Alfa AF: 0.524 Hom.: 2719

Bravo AF: 0.547

Asia WGS AF: 0.477 AC: 1656 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.6
DANN	Benign	0.88
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs4321804; hg19: chr6-92164099; COSMIC: COSV60245326;