2-118078449-C-G

Variant names:

• chr2-118078449-C-G
• rs7566605
• XR_001739662.3:n.181+9802G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001739662.3(LOC107985940):​n.181+9802G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,038 control chromosomes in the GnomAD database, including 37,662 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 0.70 (37662 hom., cov: 31)
• Consequence: LOC107985940 XR_001739662.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

Genes affected

LOC107985940 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985940	XR_001739662.3	n.181+9802G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106620 AN: 151920 Hom.: 37626 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.702 AC: 106712 AN: 152038 Hom.: 37662 Cov.: 31 AF XY: 0.702 AC XY: 52150 AN XY: 74320

Gnomad4 AFR AF: 0.760 AC: 0.75966 AN: 0.75966

Gnomad4 AMR AF: 0.716 AC: 0.716475 AN: 0.716475

Gnomad4 ASJ AF: 0.646 AC: 0.646398 AN: 0.646398

Gnomad4 EAS AF: 0.640 AC: 0.639876 AN: 0.639876

Gnomad4 SAS AF: 0.706 AC: 0.706468 AN: 0.706468

Gnomad4 FIN AF: 0.662 AC: 0.662436 AN: 0.662436

Gnomad4 NFE AF: 0.676 AC: 0.675847 AN: 0.675847

Gnomad4 OTH AF: 0.687 AC: 0.68661 AN: 0.68661

Alfa AF: 0.703 Hom.: 4673

Bravo AF: 0.705

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	16
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7566605; hg19: chr2-118836025; COSMIC: COSV60100130;