6-23467938-C-T

Variant names:

• chr6-23467938-C-T
• rs10484538
• ENST00000690652.3:n.356-10268G>A

Variant summary

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

The ENST00000690652.3(ENSG00000289368):​n.356-10268G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 152,008 control chromosomes in the GnomAD database, including 183 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 0.034 (183 hom., cov: 31)
• Consequence: ENSG00000289368 ENST00000690652.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 2 publications found

Genes affected

ENSG00000289368 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690652.3. 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
	ENSG00000289368	ENST00000690652.3		n.356-10268G>A		intron	N/A
	ENSG00000289368	ENST00000700866.2		n.181-10268G>A		intron	N/A
	ENSG00000289368	ENST00000702216.2		n.203-10268G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0341 AC: 5186 AN: 151890 Hom.: 181 Cov.: 31

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0189

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0177

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0342 AC: 5197 AN: 152008 Hom.: 183 Cov.: 31 AF XY: 0.0364 AC XY: 2704 AN XY: 74288

African (AFR) AF: 0.0390 AC: 1620 AN: 41498

American (AMR) AF: 0.0189 AC: 287 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3466

East Asian (EAS) AF: 0.207 AC: 1066 AN: 5140

South Asian (SAS) AF: 0.0956 AC: 461 AN: 4820

European-Finnish (FIN) AF: 0.0268 AC: 284 AN: 10606

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0178 AC: 1206 AN: 67942

Other (OTH) AF: 0.0318 AC: 67 AN: 2110

Alfa AF: 0.00988 Hom.: 2

Bravo AF: 0.0343

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0070
DANN	Benign	0.66
PhyloP100		-2.3

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: rs10484538;

hg19: chr6-23468166;