1-210241623-C-T

Variant names:

• chr1-210241623-C-T
• rs747812740
• NM_019605.5:c.357C>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 0P and 3B. BP4_Moderate BP7

The NM_019605.5(SERTAD4):​c.357C>T​(p.Ile119Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,459,482 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 31)
  • Exomes 𝑓: 0.000013 (0 hom.)
• Consequence: SERTAD4 NM_019605.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 0 publications found

Genes affected

SERTAD4 (HGNC:25236): (SERTA domain containing 4) Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BP7: Synonymous conserved (PhyloP=0.262 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019605.5. 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
	SERTAD4	NM_019605.5	MANE Select	c.357C>T	p.Ile119Ile	synonymous	Exon 4 of 4	NP_062551.1	Q9NUC0
	SERTAD4	NM_001375428.1		c.357C>T	p.Ile119Ile	synonymous	Exon 4 of 4	NP_001362357.1	Q9NUC0
	SERTAD4	NM_001354173.2		c.291+2015C>T		intron	N/A	NP_001341102.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERTAD4	ENST00000367012.4	TSL:1 MANE Select	c.357C>T	p.Ile119Ile	synonymous	Exon 4 of 4	ENSP00000355979.3	Q9NUC0
	SERTAD4	ENST00000933764.1		c.357C>T	p.Ile119Ile	synonymous	Exon 5 of 5	ENSP00000603823.1
	SERTAD4	ENST00000946958.1		c.357C>T	p.Ile119Ile	synonymous	Exon 4 of 4	ENSP00000617017.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD2 exomes AF: 0.0000240 AC: 6 AN: 250298 AF XY: 0.00000739

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000272

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000883

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000130 AC: 19 AN: 1459482 Hom.: 0 Cov.: 35 AF XY: 0.00000827 AC XY: 6 AN XY: 725948

African (AFR) AF: 0.00 AC: 0 AN: 33384

American (AMR) AF: 0.00 AC: 0 AN: 44562

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26030

East Asian (EAS) AF: 0.000353 AC: 14 AN: 39626

South Asian (SAS) AF: 0.00 AC: 0 AN: 85948

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53198

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5746

European-Non Finnish (NFE) AF: 0.00000450 AC: 5 AN: 1110762

Other (OTH) AF: 0.00 AC: 0 AN: 60226

GnomAD4 genome Cov.: 31

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	10
DANN	Benign	0.70
PhyloP100		0.26
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: rs747812740; hg19: chr1-210414968; COSMIC: COSV65400222;