chr2-77848118-G-A

Variant names:

• chr2-77848118-G-A
• rs7595103
• ENST00000667782.1:n.222-8228C>T

Variant summary

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

The NR_110288.1(LOC101927967):​n.428-8228C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,010 control chromosomes in the GnomAD database, including 34,358 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 0.67 (34358 hom., cov: 32)
• Consequence: LOC101927967 NR_110288.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 7 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_110288.1. 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
	LOC101927967	NR_110288.1		n.428-8228C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227088	ENST00000667782.1		n.222-8228C>T		intron	N/A
	ENSG00000227088	ENST00000759916.1		n.353-8228C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101228 AN: 151892 Hom.: 34314 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.667 AC: 101324 AN: 152010 Hom.: 34358 Cov.: 32 AF XY: 0.673 AC XY: 49977 AN XY: 74298

African (AFR) AF: 0.692 AC: 28707 AN: 41466

American (AMR) AF: 0.733 AC: 11209 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2372 AN: 3470

East Asian (EAS) AF: 0.930 AC: 4800 AN: 5164

South Asian (SAS) AF: 0.875 AC: 4221 AN: 4826

European-Finnish (FIN) AF: 0.586 AC: 6177 AN: 10548

Middle Eastern (MID) AF: 0.700 AC: 203 AN: 290

European-Non Finnish (NFE) AF: 0.613 AC: 41674 AN: 67940

Other (OTH) AF: 0.662 AC: 1399 AN: 2112

Alfa AF: 0.646 Hom.: 57258

Bravo AF: 0.675

Asia WGS AF: 0.888 AC: 3083 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.51
DANN	Benign	0.36
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs7595103; hg19: chr2-78075244;