rs4877406

Variant names:

• chr9-88145890-C-T
• rs4877406

Variant summary

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

The variant allele was found at a frequency of 0.3 in 152,090 control chromosomes in the GnomAD database, including 7,084 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 0.30 (7077 hom., cov: 32)
  • Exomes 𝑓: 0.26 (7 hom.)
• Consequence: RSRC1P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756
• Publications: 2 publications found

Genes affected

RSRC1P1 (HGNC:57037):

ENSG00000307536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826920.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307536	ENST00000826920.1		n.154+26057C>T		intron	N/A
	ENSG00000307536	ENST00000850618.1		n.477+26057C>T		intron	N/A
	ENSG00000276535	ENST00000614041.1	TSL:6	n.-40G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45539 AN: 151790 Hom.: 7066 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.261

GnomAD4 exome AF: 0.258 AC: 47 AN: 182 Hom.: 7 Cov.: 0 AF XY: 0.283 AC XY: 26 AN XY: 92

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.281 AC: 41 AN: 146

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 5 AN: 30

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.300 AC: 45594 AN: 151908 Hom.: 7077 Cov.: 32 AF XY: 0.305 AC XY: 22614 AN XY: 74228

African (AFR) AF: 0.333 AC: 13766 AN: 41400

American (AMR) AF: 0.364 AC: 5559 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3468

East Asian (EAS) AF: 0.261 AC: 1342 AN: 5150

South Asian (SAS) AF: 0.322 AC: 1552 AN: 4816

European-Finnish (FIN) AF: 0.307 AC: 3241 AN: 10542

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18680 AN: 67956

Other (OTH) AF: 0.265 AC: 558 AN: 2106

Alfa AF: 0.277 Hom.: 10220

Bravo AF: 0.304

Asia WGS AF: 0.319 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.6
DANN	Benign	0.51
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs4877406; hg19: chr9-90760805;