chr6-4623578-T-C

Variant names:

• chr6-4623578-T-C
• rs234420
• ENST00000716074.1:n.722-41775A>G

Variant summary

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

The ENST00000716074.1(ENSG00000284823):​n.722-41775A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 152,184 control chromosomes in the GnomAD database, including 1,360 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 0.079 (1360 hom., cov: 32)
• Consequence: ENSG00000284823 ENST00000716074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 0 publications found

Genes affected

ENSG00000284823 (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 (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716074.1. 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
	ENSG00000284823	ENST00000716074.1		n.722-41775A>G		intron	N/A
	ENSG00000284823	ENST00000827010.1		n.243+23973A>G		intron	N/A
	ENSG00000284823	ENST00000827011.1		n.220+23973A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0783 AC: 11903 AN: 152066 Hom.: 1354 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0347

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.0345

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00360

Gnomad OTH AF: 0.0613

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

GnomAD4 genome AF: 0.0786 AC: 11956 AN: 152184 Hom.: 1360 Cov.: 32 AF XY: 0.0780 AC XY: 5802 AN XY: 74422

African (AFR) AF: 0.255 AC: 10589 AN: 41470

American (AMR) AF: 0.0346 AC: 530 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3466

East Asian (EAS) AF: 0.0346 AC: 179 AN: 5178

South Asian (SAS) AF: 0.0444 AC: 214 AN: 4824

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10618

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00360 AC: 245 AN: 68004

Other (OTH) AF: 0.0635 AC: 134 AN: 2110

Alfa AF: 0.0439 Hom.: 212

Bravo AF: 0.0874

Asia WGS AF: 0.0760 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.35
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs234420; hg19: chr6-4623812;