rs2844573

Variant names:

• chr6-31367677-A-C
• rs2844573
• ENST00000649421.1:n.274+347A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-31367677-A-C
• chr6-31367677-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649421.1(ENSG00000285647):​n.274+347A>C variant causes a intron 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 ENST00000649421.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.645

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285647	ENST00000649421.1	n.274+347A>C		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.0957

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.169

Alfa AF: 0.252 Hom.: 2314

Bravo AF: 0.196

Asia WGS AF: 0.160 AC: 557 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844573; hg19: chr6-31335454;