chr22-39291479-A-G

Variant names:

• chr22-39291479-A-G
• rs54211
• ENST00000760985.1:n.280+2677T>C

Variant summary

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

The ENST00000760985.1(ENSG00000299144):​n.280+2677T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.905 in 152,316 control chromosomes in the GnomAD database, including 62,441 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 0.90 (62441 hom., cov: 34)
• Consequence: ENSG00000299144 ENST00000760985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 18 publications found

Genes affected

ENSG00000299144 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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
ENSG00000299144	ENST00000760985.1	n.280+2677T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137739 AN: 152198 Hom.: 62411 Cov.: 34

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.905 AC: 137820 AN: 152316 Hom.: 62441 Cov.: 34 AF XY: 0.904 AC XY: 67325 AN XY: 74464

African (AFR) AF: 0.931 AC: 38694 AN: 41572

American (AMR) AF: 0.924 AC: 14143 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3151 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5183 AN: 5184

South Asian (SAS) AF: 0.968 AC: 4675 AN: 4830

European-Finnish (FIN) AF: 0.839 AC: 8896 AN: 10604

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60051 AN: 68030

Other (OTH) AF: 0.913 AC: 1931 AN: 2114

Alfa AF: 0.896 Hom.: 202668

Bravo AF: 0.913

Asia WGS AF: 0.968 AC: 3367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.46
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs54211; hg19: chr22-39687484;