rs2377961

Variant names:

• chr18-9099556-T-C
• rs2377961
• ENST00000827765.1:n.123+2848A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-9099556-T-C
• chr18-9099556-T-G

Variant summary

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

The ENST00000827765.1(ENSG00000288939):​n.123+2848A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,054 control chromosomes in the GnomAD database, including 9,087 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 0.34 (9087 hom., cov: 32)
• Consequence: ENSG00000288939 ENST00000827765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 6 publications found

Genes affected

ENSG00000288939 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.418 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
ENSG00000288939	ENST00000827765.1	n.123+2848A>G		intron_variant	Intron 1 of 3
ENSG00000288939	ENST00000827767.1	n.100+2848A>G		intron_variant	Intron 1 of 4
ENSG00000288939	ENST00000827772.1	n.*135A>G		downstream_gene_variant
ENSG00000288939	ENST00000827773.1	n.*135A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51692 AN: 151936 Hom.: 9081 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.340 AC: 51720 AN: 152054 Hom.: 9087 Cov.: 32 AF XY: 0.338 AC XY: 25087 AN XY: 74320

African (AFR) AF: 0.354 AC: 14672 AN: 41466

American (AMR) AF: 0.426 AC: 6509 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1589 AN: 3462

East Asian (EAS) AF: 0.320 AC: 1660 AN: 5180

South Asian (SAS) AF: 0.287 AC: 1385 AN: 4826

European-Finnish (FIN) AF: 0.245 AC: 2590 AN: 10570

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22073 AN: 67968

Other (OTH) AF: 0.373 AC: 786 AN: 2110

Alfa AF: 0.330 Hom.: 29063

Bravo AF: 0.357

Asia WGS AF: 0.298 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.70
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2377961; hg19: chr18-9099554;