rs2031709

Positions:

• chr1-1550604-C-A
• chr1-1550604-C-G
• chr1-1550604-C-T

Variant summary

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

The NM_014188.3(SSU72):​c.225-5602G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0581 in 152,220 control chromosomes in the GnomAD database, including 560 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 0.058 (560 hom., cov: 32)
• Consequence: SSU72 NM_014188.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768

Genes affected

SSU72 (HGNC:25016): (SSU72 homolog, RNA polymerase II CTD phosphatase) Enables RNA polymerase II CTD heptapeptide repeat phosphatase activity. Involved in dephosphorylation of RNA polymerase II C-terminal domain and mRNA polyadenylation. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSU72	NM_014188.3	c.225-5602G>T		intron_variant		ENST00000291386.4	NP_054907.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSU72	ENST00000291386.4	c.225-5602G>T		intron_variant		1	NM_014188.3	ENSP00000291386	P1
SSU72	ENST00000378725.3	n.255-5602G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0580 AC: 8824 AN: 152100 Hom.: 556 Cov.: 32

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.0443

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0162

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0581 AC: 8846 AN: 152220 Hom.: 560 Cov.: 32 AF XY: 0.0644 AC XY: 4794 AN XY: 74420

Gnomad4 AFR AF: 0.0737

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.0443

Gnomad4 NFE AF: 0.0162

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0232 Hom.: 275

Bravo AF: 0.0613

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2031709; hg19: chr1-1485984;