6-31437840-T-C

Variant names:

• chr6-31437840-T-C
• rs2596466
• ENST00000673857.1:n.63-25283T>C

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-25283T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.055 in 152,008 control chromosomes in the GnomAD database, including 403 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 0.055 (403 hom., cov: 32)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.943
• Publications: 18 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=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.179 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.63-25283T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0551 AC: 8372 AN: 151890 Hom.: 403 Cov.: 32

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0589

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.0385

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0437

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

GnomAD4 genome AF: 0.0550 AC: 8367 AN: 152008 Hom.: 403 Cov.: 32 AF XY: 0.0578 AC XY: 4297 AN XY: 74344

African (AFR) AF: 0.0133 AC: 552 AN: 41412

American (AMR) AF: 0.0588 AC: 895 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 19 AN: 3464

East Asian (EAS) AF: 0.189 AC: 976 AN: 5162

South Asian (SAS) AF: 0.0381 AC: 184 AN: 4826

European-Finnish (FIN) AF: 0.122 AC: 1291 AN: 10594

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0640 AC: 4356 AN: 68018

Other (OTH) AF: 0.0432 AC: 91 AN: 2106

Alfa AF: 0.0507 Hom.: 347

Bravo AF: 0.0516

Asia WGS AF: 0.0620 AC: 215 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	14
DANN	Benign	0.97
PhyloP100		0.94

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: rs2596466;

hg19: chr6-31405617;