6-31420818-A-G

Variant names:

• chr6-31420818-A-G
• rs9295993
• ENST00000673857.1:n.62+20055A>G

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.62+20055A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,788 control chromosomes in the GnomAD database, including 8,349 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 0.32 (8349 hom., cov: 32)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 15 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000673857.1. 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
	ENSG00000288587	ENST00000673857.1		n.62+20055A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48500 AN: 151672 Hom.: 8331 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.320 AC: 48569 AN: 151788 Hom.: 8349 Cov.: 32 AF XY: 0.327 AC XY: 24242 AN XY: 74204

African (AFR) AF: 0.397 AC: 16400 AN: 41272

American (AMR) AF: 0.349 AC: 5300 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1216 AN: 3468

East Asian (EAS) AF: 0.317 AC: 1639 AN: 5176

South Asian (SAS) AF: 0.305 AC: 1465 AN: 4808

European-Finnish (FIN) AF: 0.370 AC: 3909 AN: 10570

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17489 AN: 67984

Other (OTH) AF: 0.310 AC: 652 AN: 2104

Alfa AF: 0.273 Hom.: 5286

Bravo AF: 0.320

Asia WGS AF: 0.361 AC: 1254 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.2
DANN	Benign	0.58
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs9295993; hg19: chr6-31388595;