rs908958

Variant names:

• chr2-76378865-C-G
• rs908958
• ENST00000654219.1:n.191-6365C>G

Your query was ambiguous. Multiple possible variants found:

• chr2-76378865-C-G
• chr2-76378865-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654219.1(ENSG00000287172):​n.191-6365C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 152,138 control chromosomes in the GnomAD database, including 48,699 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 0.80 (48699 hom., cov: 32)
• Consequence: ENSG00000287172 ENST00000654219.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

Genes affected

ENSG00000287172 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.865 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
ENSG00000287172	ENST00000654219.1	n.191-6365C>G		intron_variant	Intron 2 of 4
ENSG00000287172	ENST00000668214.1	n.163-16823C>G		intron_variant	Intron 2 of 3
ENSG00000287172	ENST00000669228.1	n.191-6387C>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120902 AN: 152020 Hom.: 48679 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.795 AC: 120966 AN: 152138 Hom.: 48699 Cov.: 32 AF XY: 0.793 AC XY: 58957 AN XY: 74368

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.814

Alfa AF: 0.832 Hom.: 6302

Bravo AF: 0.783

Asia WGS AF: 0.685 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs908958; hg19: chr2-76605991;