rs908958

Positions:

• 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, non coding transcript 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: ENST00000654219.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654219.1	n.191-6365C>G		intron_variant, non_coding_transcript_variant
	ENST00000668214.1	n.163-16823C>G		intron_variant, non_coding_transcript_variant
	ENST00000669228.1	n.191-6387C>G		intron_variant, non_coding_transcript_variant

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;