chr6-31367677-A-C

Variant names:

• chr6-31367677-A-C
• rs2844573
• ENST00000755531.1:n.1588A>C

Variant summary

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

The ENST00000755531.1(ENSG00000285647):​n.1588A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,220 control chromosomes in the GnomAD database, including 4,244 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 0.21 (4244 hom., cov: 33)
• Consequence: ENSG00000285647 ENST00000755531.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.645
• Publications: 16 publications found

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755531.1. 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
	ENSG00000285647	ENST00000755531.1		n.1588A>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000285647	ENST00000649421.2		n.274+347A>C		intron	N/A
	ENSG00000298426	ENST00000755446.1		n.326+13480A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32325 AN: 152102 Hom.: 4247 Cov.: 33

Gnomad AFR AF: 0.0958

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.212 AC: 32327 AN: 152220 Hom.: 4244 Cov.: 33 AF XY: 0.205 AC XY: 15245 AN XY: 74420

African (AFR) AF: 0.0957 AC: 3975 AN: 41554

American (AMR) AF: 0.129 AC: 1974 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3468

East Asian (EAS) AF: 0.186 AC: 965 AN: 5186

South Asian (SAS) AF: 0.124 AC: 600 AN: 4830

European-Finnish (FIN) AF: 0.264 AC: 2796 AN: 10586

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20935 AN: 67982

Other (OTH) AF: 0.169 AC: 357 AN: 2114

Alfa AF: 0.236 Hom.: 5505

Bravo AF: 0.196

Asia WGS AF: 0.160 AC: 557 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	10
DANN	Benign	0.56
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs2844573; hg19: chr6-31335454;