rs114682662

Variant names:

• chr19-49645071-G-A
• rs114682662
• NM_021228.3:c.45G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-49645071-G-A
• chr19-49645071-G-C

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_021228.3(SCAF1):​c.45G>A​(p.Gly15Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: SCAF1 NM_021228.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902

Genes affected

SCAF1 (HGNC:30403): (SR-related CTD associated factor 1) Enables RNA polymerase II C-terminal domain binding activity. Predicted to be involved in RNA splicing; mRNA processing; and transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP7: Synonymous conserved (PhyloP=-0.902 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCAF1	NM_021228.3	c.45G>A	p.Gly15Gly	synonymous_variant	Exon 2 of 11	ENST00000360565.8	NP_067051.2
SCAF1	XM_011527194.4	c.54G>A	p.Gly18Gly	synonymous_variant	Exon 2 of 11		XP_011525496.1
SCAF1	XM_005259122.6	c.45G>A	p.Gly15Gly	synonymous_variant	Exon 2 of 11		XP_005259179.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCAF1	ENST00000360565.8	c.45G>A	p.Gly15Gly	synonymous_variant	Exon 2 of 11	2	NM_021228.3	ENSP00000353769.2
SCAF1	ENST00000598359.5	c.45G>A	p.Gly15Gly	synonymous_variant	Exon 2 of 7	3		ENSP00000473210.1
SCAF1	ENST00000595242.3	c.45G>A	p.Gly15Gly	synonymous_variant	Exon 1 of 4	3		ENSP00000472276.1
SCAF1	ENST00000601038.5	c.45G>A	p.Gly15Gly	synonymous_variant	Exon 1 of 4	3		ENSP00000472649.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	5.3
DANN	Benign	0.74
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs114682662; hg19: chr19-50148328;