rs7285004

Variant names:

• chr22-44378820-T-C
• rs7285004
• ENST00000777997.1:n.288-9637A>G

Variant summary

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

The ENST00000777997.1(ENSG00000301322):​n.288-9637A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,038 control chromosomes in the GnomAD database, including 12,572 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 0.40 (12572 hom., cov: 32)
• Consequence: ENSG00000301322 ENST00000777997.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 3 publications found

Genes affected

ENSG00000301322 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777997.1. 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
	ENSG00000301322	ENST00000777997.1		n.288-9637A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60092 AN: 151920 Hom.: 12561 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.396 AC: 60137 AN: 152038 Hom.: 12572 Cov.: 32 AF XY: 0.402 AC XY: 29868 AN XY: 74320

African (AFR) AF: 0.328 AC: 13614 AN: 41472

American (AMR) AF: 0.562 AC: 8574 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3470

East Asian (EAS) AF: 0.613 AC: 3173 AN: 5172

South Asian (SAS) AF: 0.506 AC: 2434 AN: 4814

European-Finnish (FIN) AF: 0.396 AC: 4181 AN: 10562

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.379 AC: 25740 AN: 67966

Other (OTH) AF: 0.403 AC: 851 AN: 2112

Alfa AF: 0.389 Hom.: 31593

Bravo AF: 0.407

Asia WGS AF: 0.555 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.48
PhyloP100		-0.094

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: rs7285004;

hg19: chr22-44774700;