20-7831703-T-C

Variant names:

• chr20-7831703-T-C
• rs2423279

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 0.292 in 294,204 control chromosomes in the GnomAD database, including 13,942 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 0.29 (6895 hom., cov: 33)
  • Exomes 𝑓: 0.29 (7047 hom.)
• Consequence: SRSF10P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 68 publications found

Genes affected

SRSF10P2 (HGNC:24823):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000400616.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRSF10P2	ENST00000400616.2	TSL:6	n.*95A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44535 AN: 152020 Hom.: 6874 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.309

GnomAD4 exome AF: 0.290 AC: 41269 AN: 142066 Hom.: 7047 AF XY: 0.303 AC XY: 23257 AN XY: 76826

African (AFR) AF: 0.350 AC: 1732 AN: 4946

American (AMR) AF: 0.336 AC: 3156 AN: 9398

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1329 AN: 4226

East Asian (EAS) AF: 0.293 AC: 2891 AN: 9860

South Asian (SAS) AF: 0.474 AC: 8927 AN: 18822

European-Finnish (FIN) AF: 0.213 AC: 1688 AN: 7910

Middle Eastern (MID) AF: 0.335 AC: 181 AN: 540

European-Non Finnish (NFE) AF: 0.244 AC: 19224 AN: 78818

Other (OTH) AF: 0.284 AC: 2141 AN: 7546

GnomAD4 genome AF: 0.293 AC: 44605 AN: 152138 Hom.: 6895 Cov.: 33 AF XY: 0.293 AC XY: 21759 AN XY: 74386

African (AFR) AF: 0.353 AC: 14663 AN: 41490

American (AMR) AF: 0.306 AC: 4681 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1680 AN: 5168

South Asian (SAS) AF: 0.486 AC: 2346 AN: 4826

European-Finnish (FIN) AF: 0.205 AC: 2175 AN: 10606

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16878 AN: 67974

Other (OTH) AF: 0.316 AC: 668 AN: 2112

Alfa AF: 0.268 Hom.: 13490

Bravo AF: 0.302

Asia WGS AF: 0.446 AC: 1548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.7
DANN	Benign	0.42
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs2423279; hg19: chr20-7812350; COSMIC: COSV68763360;