10-89979068-T-C

Variant names:

• chr10-89979068-T-C
• rs11812465
• ENST00000489253.1:n.352T>C

Variant summary

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

The ENST00000489253.1(SNRPD2P1):​n.352T>C variant causes a splice region, non coding transcript exon change. The variant allele was found at a frequency of 0.272 in 679,664 control chromosomes in the GnomAD database, including 27,878 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 0.25 (5373 hom., cov: 31)
  • Exomes 𝑓: 0.28 (22505 hom.)
• Consequence: SNRPD2P1 ENST00000489253.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.36
• Publications: 4 publications found

Genes affected

SNRPD2P1 (HGNC:31459): (small nuclear ribonucleoprotein D2 pseudogene 1)

LINC00865 (HGNC:45170): (long intergenic non-protein coding RNA 865)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000489253.1. 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
	SNRPD2P1	ENST00000489253.1	TSL:6	n.352T>C		splice_region non_coding_transcript_exon	Exon 1 of 1
	LINC00865	ENST00000664430.1		n.548+64298T>C		intron	N/A
	LINC00865	ENST00000715760.1		n.741-40767T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38263 AN: 151520 Hom.: 5361 Cov.: 31

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.0304

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.266

GnomAD4 exome AF: 0.278 AC: 146635 AN: 528024 Hom.: 22505 Cov.: 4 AF XY: 0.280 AC XY: 79865 AN XY: 285550

African (AFR) AF: 0.173 AC: 2604 AN: 15066

American (AMR) AF: 0.162 AC: 5377 AN: 33152

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 5312 AN: 15174

East Asian (EAS) AF: 0.0184 AC: 620 AN: 33758

South Asian (SAS) AF: 0.236 AC: 12643 AN: 53564

European-Finnish (FIN) AF: 0.324 AC: 14378 AN: 44328

Middle Eastern (MID) AF: 0.331 AC: 1209 AN: 3658

European-Non Finnish (NFE) AF: 0.320 AC: 96489 AN: 301070

Other (OTH) AF: 0.283 AC: 8003 AN: 28254

GnomAD4 genome AF: 0.253 AC: 38291 AN: 151640 Hom.: 5373 Cov.: 31 AF XY: 0.252 AC XY: 18625 AN XY: 74048

African (AFR) AF: 0.165 AC: 6793 AN: 41286

American (AMR) AF: 0.213 AC: 3242 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1254 AN: 3462

East Asian (EAS) AF: 0.0299 AC: 154 AN: 5152

South Asian (SAS) AF: 0.241 AC: 1155 AN: 4784

European-Finnish (FIN) AF: 0.339 AC: 3552 AN: 10486

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.312 AC: 21194 AN: 67932

Other (OTH) AF: 0.275 AC: 579 AN: 2106

Alfa AF: 0.278 Hom.: 3915

Bravo AF: 0.240

Asia WGS AF: 0.198 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	5.6
DANN	Benign	0.57
PhyloP100		5.4

Splicing

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

Other links and lift over

dbSNP: rs11812465; hg19: chr10-91738825;