6-104465169-A-G

Variant names:

• chr6-104465169-A-G
• rs408949
• ENST00000799445.1:n.1246-2046T>C

Variant summary

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

The ENST00000799445.1(ENSG00000287616):​n.1246-2046T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,146 control chromosomes in the GnomAD database, including 48,723 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 0.80 (48723 hom., cov: 33)
• Consequence: ENSG00000287616 ENST00000799445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 5 publications found

Genes affected

ENSG00000287616 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000799445.1. 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
	ENSG00000287616	ENST00000799445.1		n.1246-2046T>C		intron	N/A
	ENSG00000287616	ENST00000799447.1		n.406-2046T>C		intron	N/A
	ENSG00000287616	ENST00000799449.1		n.528-2046T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121124 AN: 152028 Hom.: 48674 Cov.: 33

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.797 AC: 121234 AN: 152146 Hom.: 48723 Cov.: 33 AF XY: 0.800 AC XY: 59525 AN XY: 74378

African (AFR) AF: 0.683 AC: 28356 AN: 41498

American (AMR) AF: 0.877 AC: 13400 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2929 AN: 3468

East Asian (EAS) AF: 0.823 AC: 4250 AN: 5162

South Asian (SAS) AF: 0.797 AC: 3846 AN: 4826

European-Finnish (FIN) AF: 0.834 AC: 8835 AN: 10590

Middle Eastern (MID) AF: 0.918 AC: 268 AN: 292

European-Non Finnish (NFE) AF: 0.834 AC: 56741 AN: 68002

Other (OTH) AF: 0.847 AC: 1788 AN: 2110

Alfa AF: 0.832 Hom.: 70807

Bravo AF: 0.798

Asia WGS AF: 0.819 AC: 2843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.3
DANN	Benign	0.87
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs408949; hg19: chr6-104913044;