6-91408059-T-C

Variant names:

• chr6-91408059-T-C
• rs9351265
• ENST00000721215.1:n.108-17137T>C

Variant summary

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

The ENST00000721215.1(ENSG00000294116):​n.108-17137T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,008 control chromosomes in the GnomAD database, including 14,035 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 0.42 (14035 hom., cov: 32)
• Consequence: ENSG00000294116 ENST00000721215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 3 publications found

Genes affected

ENSG00000294116 (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 (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000721215.1. 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
	ENSG00000294116	ENST00000721215.1		n.108-17137T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64224 AN: 151890 Hom.: 14027 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.423 AC: 64242 AN: 152008 Hom.: 14035 Cov.: 32 AF XY: 0.428 AC XY: 31834 AN XY: 74294

African (AFR) AF: 0.334 AC: 13844 AN: 41468

American (AMR) AF: 0.514 AC: 7843 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1768 AN: 3464

East Asian (EAS) AF: 0.577 AC: 2981 AN: 5164

South Asian (SAS) AF: 0.484 AC: 2333 AN: 4816

European-Finnish (FIN) AF: 0.487 AC: 5146 AN: 10560

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.427 AC: 28996 AN: 67956

Other (OTH) AF: 0.417 AC: 879 AN: 2108

Alfa AF: 0.401 Hom.: 5327

Bravo AF: 0.422

Asia WGS AF: 0.483 AC: 1676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.14
PhyloP100		0.31

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: rs9351265;

hg19: chr6-92117777;