rs4880711

Variant names:

• chr10-5185908-T-C
• rs4880711

Your query was ambiguous. Multiple possible variants found:

• chr10-5185908-T-C
• chr10-5185908-T-G

Variant summary

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

The variant allele was found at a frequency of 0.303 in 152,064 control chromosomes in the GnomAD database, including 7,541 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 (7541 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 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

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46058 AN: 151946 Hom.: 7535 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.303 AC: 46090 AN: 152064 Hom.: 7541 Cov.: 32 AF XY: 0.302 AC XY: 22417 AN XY: 74300

African (AFR) AF: 0.261 AC: 10813 AN: 41476

American (AMR) AF: 0.251 AC: 3826 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 827 AN: 3468

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5182

South Asian (SAS) AF: 0.182 AC: 875 AN: 4818

European-Finnish (FIN) AF: 0.403 AC: 4250 AN: 10548

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.361 AC: 24560 AN: 67984

Other (OTH) AF: 0.261 AC: 553 AN: 2116

Alfa AF: 0.214 Hom.: 519

Bravo AF: 0.288

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	16
DANN	Benign	0.94
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs4880711; hg19: chr10-5227871;