7-50189102-C-T

Variant names:

• chr7-50189102-C-T
• rs921916
• ENST00000774254.1:n.255+8312G>A

Variant summary

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

The ENST00000774254.1(ENSG00000300822):​n.255+8312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,178 control chromosomes in the GnomAD database, including 51,568 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 0.82 (51568 hom., cov: 33)
• Consequence: ENSG00000300822 ENST00000774254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 8 publications found

Genes affected

ENSG00000300822 (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 (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774254.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300822	ENST00000774254.1		n.255+8312G>A		intron	N/A
	ENSG00000300822	ENST00000774255.1		n.171+8312G>A		intron	N/A
	ENSG00000300822	ENST00000774256.1		n.181+8312G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125126 AN: 152060 Hom.: 51527 Cov.: 33

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.823 AC: 125226 AN: 152178 Hom.: 51568 Cov.: 33 AF XY: 0.823 AC XY: 61259 AN XY: 74394

African (AFR) AF: 0.808 AC: 33513 AN: 41480

American (AMR) AF: 0.838 AC: 12824 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2497 AN: 3470

East Asian (EAS) AF: 0.969 AC: 5029 AN: 5190

South Asian (SAS) AF: 0.764 AC: 3686 AN: 4822

European-Finnish (FIN) AF: 0.849 AC: 9000 AN: 10598

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56069 AN: 67998

Other (OTH) AF: 0.798 AC: 1687 AN: 2114

Alfa AF: 0.813 Hom.: 25252

Bravo AF: 0.822

Asia WGS AF: 0.870 AC: 3027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.77
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs921916; hg19: chr7-50228698;