6-110957717-A-G

Variant names:

• chr6-110957717-A-G
• rs6902336
• ENST00000758068.1:n.129+1321T>C

Variant summary

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

The ENST00000758068.1(ENSG00000298809):​n.129+1321T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 144,682 control chromosomes in the GnomAD database, including 8,258 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 0.33 (8258 hom., cov: 32)
• Consequence: ENSG00000298809 ENST00000758068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 0 publications found

Genes affected

ENSG00000298809 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758068.1. 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
	ENSG00000298809	ENST00000758068.1		n.129+1321T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.331 AC: 47827 AN: 144564 Hom.: 8243 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.331 AC: 47894 AN: 144682 Hom.: 8258 Cov.: 32 AF XY: 0.334 AC XY: 23545 AN XY: 70426

African (AFR) AF: 0.475 AC: 19412 AN: 40898

American (AMR) AF: 0.219 AC: 3216 AN: 14696

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 955 AN: 3432

East Asian (EAS) AF: 0.464 AC: 1338 AN: 2884

South Asian (SAS) AF: 0.447 AC: 2015 AN: 4504

European-Finnish (FIN) AF: 0.316 AC: 3092 AN: 9782

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 16971 AN: 65404

Other (OTH) AF: 0.315 AC: 635 AN: 2016

Alfa AF: 0.0163 Hom.: 21

Bravo AF: 0.342

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.14
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6902336; hg19: chr6-111278920;