6-23135698-T-C

Variant names:

• chr6-23135698-T-C
• rs4626416
• ENST00000797408.1:n.235+39556A>G

Variant summary

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

The ENST00000797408.1(ENSG00000233358):​n.235+39556A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 151,812 control chromosomes in the GnomAD database, including 15,451 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 0.44 (15451 hom., cov: 32)
• Consequence: ENSG00000233358 ENST00000797408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 1 publications found

Genes affected

ENSG00000233358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797408.1. 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
	ENSG00000233358	ENST00000797408.1		n.235+39556A>G		intron	N/A
	ENSG00000233358	ENST00000797409.1		n.215+39556A>G		intron	N/A
	ENSG00000233358	ENST00000797410.1		n.649+39556A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66811 AN: 151694 Hom.: 15413 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.441 AC: 66898 AN: 151812 Hom.: 15451 Cov.: 32 AF XY: 0.445 AC XY: 33033 AN XY: 74192

African (AFR) AF: 0.527 AC: 21813 AN: 41418

American (AMR) AF: 0.499 AC: 7616 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1104 AN: 3470

East Asian (EAS) AF: 0.724 AC: 3741 AN: 5168

South Asian (SAS) AF: 0.320 AC: 1543 AN: 4824

European-Finnish (FIN) AF: 0.427 AC: 4492 AN: 10514

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25138 AN: 67856

Other (OTH) AF: 0.450 AC: 946 AN: 2104

Alfa AF: 0.390 Hom.: 6465

Bravo AF: 0.456

Asia WGS AF: 0.542 AC: 1876 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.57
PhyloP100		-0.42

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: rs4626416;

hg19: chr6-23135926;