chr6-24116622-T-C

Variant names:

• chr6-24116622-T-C
• rs10484657
• ENST00000810475.1:n.94-3816T>C

Variant summary

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

The ENST00000810475.1(ENSG00000305332):​n.94-3816T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0414 in 98,652 control chromosomes in the GnomAD database, including 90 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 0.041 (90 hom., cov: 33)
• Consequence: ENSG00000305332 ENST00000810475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534
• Publications: 2 publications found

Genes affected

ENSG00000305332 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810475.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305332	ENST00000810475.1		n.94-3816T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0415 AC: 4087 AN: 98554 Hom.: 90 Cov.: 33

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0282

Gnomad ASJ AF: 0.00466

Gnomad EAS AF: 0.000306

Gnomad SAS AF: 0.000466

Gnomad FIN AF: 0.00649

Gnomad MID AF: 0.0225

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0398

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

GnomAD4 genome AF: 0.0414 AC: 4084 AN: 98652 Hom.: 90 Cov.: 33 AF XY: 0.0393 AC XY: 1849 AN XY: 47016

African (AFR) AF: 0.0914 AC: 2481 AN: 27154

American (AMR) AF: 0.0281 AC: 251 AN: 8928

Ashkenazi Jewish (ASJ) AF: 0.00466 AC: 12 AN: 2574

East Asian (EAS) AF: 0.000307 AC: 1 AN: 3254

South Asian (SAS) AF: 0.000466 AC: 1 AN: 2146

European-Finnish (FIN) AF: 0.00649 AC: 34 AN: 5238

Middle Eastern (MID) AF: 0.0245 AC: 5 AN: 204

European-Non Finnish (NFE) AF: 0.0265 AC: 1247 AN: 47120

Other (OTH) AF: 0.0394 AC: 52 AN: 1320

Alfa AF: 0.0225 Hom.: 35

Bravo AF: 0.0291

Asia WGS AF: 0.00173 AC: 6 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.38
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs10484657; hg19: chr6-24116850;