rs1322849

Variant names:

• chr7-82452223-C-T
• rs1322849
• ENST00000772831.1:n.74+8274C>T

Variant summary

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

The ENST00000772831.1(ENSG00000300590):​n.74+8274C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,912 control chromosomes in the GnomAD database, including 11,542 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 0.31 (11542 hom., cov: 32)
• Consequence: ENSG00000300590 ENST00000772831.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• Publications: 3 publications found

Genes affected

ENSG00000300590 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 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
ENSG00000300590	ENST00000772831.1	n.74+8274C>T		intron_variant	Intron 1 of 2
ENSG00000300590	ENST00000772832.1	n.65+8274C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47040 AN: 151794 Hom.: 11508 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.310 AC: 47124 AN: 151912 Hom.: 11542 Cov.: 32 AF XY: 0.304 AC XY: 22549 AN XY: 74244

African (AFR) AF: 0.681 AC: 28180 AN: 41402

American (AMR) AF: 0.205 AC: 3133 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3470

East Asian (EAS) AF: 0.0128 AC: 66 AN: 5172

South Asian (SAS) AF: 0.0927 AC: 447 AN: 4820

European-Finnish (FIN) AF: 0.159 AC: 1671 AN: 10540

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.174 AC: 11809 AN: 67942

Other (OTH) AF: 0.280 AC: 590 AN: 2108

Alfa AF: 0.258 Hom.: 1105

Bravo AF: 0.330

Asia WGS AF: 0.0970 AC: 335 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.60
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1322849; hg19: chr7-82081539;