6-31422007-A-G

Variant names:

• chr6-31422007-A-G
• rs2844511
• ENST00000673857.1:n.62+21244A>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+21244A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,404 control chromosomes in the GnomAD database, including 32,099 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 0.64 (32099 hom., cov: 30)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 36 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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.775 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+21244A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.640 AC: 96895 AN: 151286 Hom.: 32054 Cov.: 30

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.811

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.641 AC: 96996 AN: 151404 Hom.: 32099 Cov.: 30 AF XY: 0.652 AC XY: 48200 AN XY: 73974

African (AFR) AF: 0.702 AC: 28864 AN: 41122

American (AMR) AF: 0.781 AC: 11812 AN: 15130

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2845 AN: 3464

East Asian (EAS) AF: 0.786 AC: 4038 AN: 5138

South Asian (SAS) AF: 0.797 AC: 3828 AN: 4806

European-Finnish (FIN) AF: 0.601 AC: 6323 AN: 10526

Middle Eastern (MID) AF: 0.803 AC: 233 AN: 290

European-Non Finnish (NFE) AF: 0.545 AC: 37024 AN: 67912

Other (OTH) AF: 0.725 AC: 1525 AN: 2104

Alfa AF: 0.600 Hom.: 29423

Bravo AF: 0.658

Asia WGS AF: 0.821 AC: 2853 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	2.7
DANN	Benign	0.65
PhyloP100		0.045

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: rs2844511;

hg19: chr6-31389784;