6-5952358-C-T

Variant names:

• chr6-5952358-C-T
• rs4960147
• ENST00000767948.1:n.1212-45458C>T

Variant summary

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

The ENST00000767948.1(ENSG00000300014):​n.1212-45458C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,000 control chromosomes in the GnomAD database, including 28,510 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 0.61 (28510 hom., cov: 32)
• Consequence: ENSG00000300014 ENST00000767948.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 3 publications found

Genes affected

ENSG00000300014 (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 = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767948.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300014	ENST00000767948.1		n.1212-45458C>T		intron	N/A
	ENSG00000300014	ENST00000767949.1		n.686-43315C>T		intron	N/A
	ENSG00000300014	ENST00000767950.1		n.940-43315C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92324 AN: 151880 Hom.: 28497 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.608 AC: 92392 AN: 152000 Hom.: 28510 Cov.: 32 AF XY: 0.601 AC XY: 44621 AN XY: 74306

African (AFR) AF: 0.715 AC: 29620 AN: 41430

American (AMR) AF: 0.567 AC: 8672 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2028 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2174 AN: 5166

South Asian (SAS) AF: 0.505 AC: 2434 AN: 4818

European-Finnish (FIN) AF: 0.544 AC: 5757 AN: 10574

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39884 AN: 67948

Other (OTH) AF: 0.599 AC: 1262 AN: 2106

Alfa AF: 0.590 Hom.: 13557

Bravo AF: 0.616

Asia WGS AF: 0.505 AC: 1758 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	0.071
DANN	Benign	0.53
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4960147; hg19: chr6-5952591;