rs4961280

Positions:

• chr8-140637315-C-A
• chr8-140637315-C-T

Variant summary

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

The NR_170171.1(ERICD):​n.3081C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,220 control chromosomes in the GnomAD database, including 2,457 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 0.16 (2456 hom., cov: 32)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: ERICD NR_170171.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

ERICD (HGNC:49404): (E2F1-regulated inhibitor of cell death)

AGO2 (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 (AMR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERICD	NR_170171.1	n.3081C>A		non_coding_transcript_exon_variant	1/1
AGO2	XM_011516968.3	c.-117+4878G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERICD	ENST00000623655.2	n.1035C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24328 AN: 152034 Hom.: 2446 Cov.: 32

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.162

GnomAD4 exome AF: 0.250 AC: 17 AN: 68 Hom.: 1 Cov.: 0 AF XY: 0.229 AC XY: 11 AN XY: 48

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 FIN exome AF: 0.292

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.375

GnomAD4 genome AF: 0.160 AC: 24337 AN: 152152 Hom.: 2456 Cov.: 32 AF XY: 0.164 AC XY: 12190 AN XY: 74376

Gnomad4 AFR AF: 0.0539

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.163

Alfa AF: 0.0633 Hom.: 76

Bravo AF: 0.161

Asia WGS AF: 0.170 AC: 591 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	0.061
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4961280; hg19: chr8-141647414;