rs6457375

Variant names:

• chr6-31304835-G-A
• rs6457375
• ENST00000755297.1:n.32+33729G>A

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+33729G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 151,894 control chromosomes in the GnomAD database, including 23,462 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 0.55 (23462 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 12 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. 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
	ENSG00000298396	ENST00000755297.1		n.32+33729G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83873 AN: 151776 Hom.: 23434 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.553 AC: 83939 AN: 151894 Hom.: 23462 Cov.: 31 AF XY: 0.554 AC XY: 41131 AN XY: 74240

African (AFR) AF: 0.611 AC: 25302 AN: 41436

American (AMR) AF: 0.603 AC: 9207 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1805 AN: 3466

East Asian (EAS) AF: 0.445 AC: 2291 AN: 5144

South Asian (SAS) AF: 0.574 AC: 2763 AN: 4814

European-Finnish (FIN) AF: 0.575 AC: 6067 AN: 10552

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34762 AN: 67904

Other (OTH) AF: 0.564 AC: 1192 AN: 2112

Alfa AF: 0.517 Hom.: 9395

Bravo AF: 0.558

Asia WGS AF: 0.537 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.7
DANN	Benign	0.58
PhyloP100		-0.069

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: rs6457375;

hg19: chr6-31272612;

COSMIC: COSV69706126;

COSMIC: COSV69706126;