rs2079604208

Variant names:

• chr19-40423102-C-G
• rs2079604208
• NM_013376.4:c.445G>C

Your query was ambiguous. Multiple possible variants found:

• chr19-40423102-C-G
• chr19-40423102-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_013376.4(SERTAD1):​c.445G>C​(p.Ala149Pro) variant causes a missense 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. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: SERTAD1 NM_013376.4 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0590
• Publications: 0 publications found

Genes affected

SERTAD1 (HGNC:17932): (SERTA domain containing 1) Predicted to be involved in epigenetic maintenance of chromatin in transcription-competent conformation. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.03993371).
• BP6: Variant 19-40423102-C-G is Benign according to our data. Variant chr19-40423102-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2253138.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013376.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERTAD1	NM_013376.4	MANE Select	c.445G>C	p.Ala149Pro	missense	Exon 2 of 2	NP_037508.2	Q9UHV2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERTAD1	ENST00000357949.5	TSL:1 MANE Select	c.445G>C	p.Ala149Pro	missense	Exon 2 of 2	ENSP00000350633.4	Q9UHV2
	SERTAD1	ENST00000869921.1		c.445G>C	p.Ala149Pro	missense	Exon 2 of 2	ENSP00000539980.1
	SERTAD1	ENST00000869922.1		c.445G>C	p.Ala149Pro	missense	Exon 2 of 2	ENSP00000539981.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.054
BayesDel_addAF	Benign	-0.34	T
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.37
DANN	Benign	0.30
DEOGEN2	Benign	0.055	T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.0031	N
LIST_S2	Benign	0.53	T
M_CAP	Benign	0.0024	T
MetaRNN	Benign	0.040	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-1.4	N
PhyloP100		-0.059
PrimateAI	Benign	0.40	T
PROVEAN	Benign	1.4	N
REVEL	Benign	0.025
Sift	Benign	0.32	T
Sift4G	Benign	0.28	T
Polyphen		0.0	B
Vest4		0.051
MutPred		0.31		Gain of glycosylation at A149 (P = 0.0217)
MVP		0.18
MPC		0.39
ClinPred		0.063	T
GERP RS		-6.4
Varity_R		0.034
gMVP		0.42
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs2079604208; hg19: chr19-40929009;