chr6-60808415-T-C

Variant names:

• chr6-60808415-T-C
• rs4098822
• ENST00000665994.1:n.168+13650T>C

Variant summary

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

The ENST00000665994.1(ENSG00000287598):​n.168+13650T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,846 control chromosomes in the GnomAD database, including 21,305 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 0.52 (21305 hom., cov: 32)
• Consequence: ENSG00000287598 ENST00000665994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341
• Publications: 4 publications found

Genes affected

ENSG00000287598 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665994.1. 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
	ENSG00000287598	ENST00000665994.1		n.168+13650T>C		intron	N/A
	ENSG00000287598	ENST00000745649.1		n.123+13650T>C		intron	N/A
	ENSG00000287598	ENST00000745650.1		n.190+13650T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79486 AN: 151728 Hom.: 21280 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.524 AC: 79562 AN: 151846 Hom.: 21305 Cov.: 32 AF XY: 0.521 AC XY: 38674 AN XY: 74208

African (AFR) AF: 0.616 AC: 25539 AN: 41436

American (AMR) AF: 0.443 AC: 6740 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1930 AN: 3472

East Asian (EAS) AF: 0.271 AC: 1396 AN: 5146

South Asian (SAS) AF: 0.469 AC: 2261 AN: 4826

European-Finnish (FIN) AF: 0.544 AC: 5740 AN: 10544

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34465 AN: 67888

Other (OTH) AF: 0.483 AC: 1022 AN: 2114

Alfa AF: 0.519 Hom.: 29972

Bravo AF: 0.520

Asia WGS AF: 0.420 AC: 1461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.56
PhyloP100		-0.34

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4098822;

hg19: chr6-57776162;