chr6-54721839-C-T

Variant names:

• chr6-54721839-C-T
• rs9474972
• ENST00000763589.1:n.133-18535G>A

Variant summary

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

The ENST00000763589.1(ENSG00000299445):​n.133-18535G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,930 control chromosomes in the GnomAD database, including 18,462 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 0.48 (18462 hom., cov: 31)
• Consequence: ENSG00000299445 ENST00000763589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 6 publications found

Genes affected

ENSG00000299445 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986606	XR_001744176.3	n.96-66162G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299445	ENST00000763589.1	n.133-18535G>A		intron_variant	Intron 1 of 6
ENSG00000299445	ENST00000763590.1	n.88-18535G>A		intron_variant	Intron 1 of 5
ENSG00000299445	ENST00000763591.1	n.70-66162G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72539 AN: 151812 Hom.: 18453 Cov.: 31

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.478 AC: 72575 AN: 151930 Hom.: 18462 Cov.: 31 AF XY: 0.476 AC XY: 35339 AN XY: 74230

African (AFR) AF: 0.335 AC: 13865 AN: 41440

American (AMR) AF: 0.382 AC: 5823 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1940 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1186 AN: 5146

South Asian (SAS) AF: 0.542 AC: 2613 AN: 4820

European-Finnish (FIN) AF: 0.578 AC: 6099 AN: 10554

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39242 AN: 67950

Other (OTH) AF: 0.458 AC: 966 AN: 2108

Alfa AF: 0.523 Hom.: 11961

Bravo AF: 0.452

Asia WGS AF: 0.392 AC: 1362 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.89
DANN	Benign	0.75
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs9474972; hg19: chr6-54586637; COSMIC: COSV107166895;