8-2202177-C-G

Variant names:

• chr8-2202177-C-G
• rs1478960
• ENST00000776944.1:n.1101C>G

Variant summary

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

The ENST00000776944.1(ENSG00000288782):​n.1101C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,138 control chromosomes in the GnomAD database, including 1,407 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 0.10 (1407 hom., cov: 33)
• Consequence: ENSG00000288782 ENST00000776944.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 2 publications found

Genes affected

ENSG00000288782 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776944.1. 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
	ENSG00000288782	ENST00000776944.1		n.1101C>G		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000288782	ENST00000776942.1		n.211-896C>G		intron	N/A
	ENSG00000288782	ENST00000776943.1		n.452-896C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15927 AN: 152020 Hom.: 1403 Cov.: 33

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0437

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0958

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0497

Gnomad OTH AF: 0.0766

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

GnomAD4 genome AF: 0.105 AC: 15944 AN: 152138 Hom.: 1407 Cov.: 33 AF XY: 0.105 AC XY: 7836 AN XY: 74370

African (AFR) AF: 0.233 AC: 9651 AN: 41492

American (AMR) AF: 0.0469 AC: 717 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0437 AC: 151 AN: 3458

East Asian (EAS) AF: 0.127 AC: 661 AN: 5186

South Asian (SAS) AF: 0.0958 AC: 460 AN: 4800

European-Finnish (FIN) AF: 0.0672 AC: 713 AN: 10604

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.0497 AC: 3381 AN: 68002

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.0812 Hom.: 105

Bravo AF: 0.109

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1478960; hg19: chr8-2149816;