6-90708033-G-T

Variant names:

• chr6-90708033-G-T
• rs713155
• ENST00000828102.1:n.522+34472G>T

Variant summary

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

The ENST00000828102.1(ENSG00000307717):​n.522+34472G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,854 control chromosomes in the GnomAD database, including 10,517 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 0.37 (10517 hom., cov: 31)
• Consequence: ENSG00000307717 ENST00000828102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405
• Publications: 10 publications found

Genes affected

ENSG00000307717 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000828102.1. 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
	ENSG00000307717	ENST00000828102.1		n.522+34472G>T		intron	N/A
	ENSG00000307717	ENST00000828103.1		n.100+34207G>T		intron	N/A
	ENSG00000307717	ENST00000828104.1		n.95+32776G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56048 AN: 151734 Hom.: 10505 Cov.: 31

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.369 AC: 56103 AN: 151854 Hom.: 10517 Cov.: 31 AF XY: 0.371 AC XY: 27535 AN XY: 74216

African (AFR) AF: 0.335 AC: 13885 AN: 41394

American (AMR) AF: 0.429 AC: 6541 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1143 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1364 AN: 5142

South Asian (SAS) AF: 0.368 AC: 1777 AN: 4824

European-Finnish (FIN) AF: 0.408 AC: 4300 AN: 10534

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25835 AN: 67940

Other (OTH) AF: 0.366 AC: 769 AN: 2102

Alfa AF: 0.372 Hom.: 19153

Bravo AF: 0.378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	1.7
DANN	Benign	0.78
PhyloP100		0.41

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: rs713155;

hg19: chr6-91417752;

COSMIC: COSV69412653;