6-31273182-C-G

Variant names:

• chr6-31273182-C-G
• rs7773175
• ENST00000755297.1:n.32+2076C>G

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+2076C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,792 control chromosomes in the GnomAD database, including 5,440 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 0.26 (5440 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 9 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298396	ENST00000755297.1		n.32+2076C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.264 AC: 39996 AN: 151672 Hom.: 5438 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.264 AC: 39999 AN: 151792 Hom.: 5440 Cov.: 31 AF XY: 0.260 AC XY: 19317 AN XY: 74192

African (AFR) AF: 0.228 AC: 9418 AN: 41378

American (AMR) AF: 0.251 AC: 3828 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1815 AN: 3464

East Asian (EAS) AF: 0.225 AC: 1165 AN: 5174

South Asian (SAS) AF: 0.333 AC: 1598 AN: 4796

European-Finnish (FIN) AF: 0.174 AC: 1829 AN: 10518

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19328 AN: 67876

Other (OTH) AF: 0.278 AC: 588 AN: 2114

Alfa AF: 0.132 Hom.: 227

Bravo AF: 0.266

Asia WGS AF: 0.268 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.048
DANN	Benign	0.31
PhyloP100		-1.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7773175; hg19: chr6-31240959;