2-77865386-C-T

Variant names:

• chr2-77865386-C-T
• rs6716793
• ENST00000667782.1:n.221+9594G>A

Variant summary

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

The ENST00000667782.1(ENSG00000227088):​n.221+9594G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,122 control chromosomes in the GnomAD database, including 58,564 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 0.88 (58564 hom., cov: 31)
• Consequence: ENSG00000227088 ENST00000667782.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 0 publications found

Genes affected

ENSG00000227088 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927967	NR_110288.1	n.427+9594G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227088	ENST00000667782.1	n.221+9594G>A		intron_variant	Intron 3 of 6
ENSG00000227088	ENST00000759916.1	n.352+9594G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133001 AN: 152004 Hom.: 58509 Cov.: 31

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.875 AC: 133112 AN: 152122 Hom.: 58564 Cov.: 31 AF XY: 0.877 AC XY: 65199 AN XY: 74350

African (AFR) AF: 0.964 AC: 40052 AN: 41536

American (AMR) AF: 0.800 AC: 12209 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2883 AN: 3468

East Asian (EAS) AF: 0.952 AC: 4904 AN: 5152

South Asian (SAS) AF: 0.913 AC: 4403 AN: 4820

European-Finnish (FIN) AF: 0.870 AC: 9189 AN: 10558

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56555 AN: 68004

Other (OTH) AF: 0.875 AC: 1850 AN: 2114

Alfa AF: 0.846 Hom.: 176470

Bravo AF: 0.874

Asia WGS AF: 0.936 AC: 3248 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.30
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6716793; hg19: chr2-78092512;