rs308207

Variant names:

• chr5-94396280-A-C
• rs308207
• NM_001145678.3:c.3117T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-94396280-A-C
• chr5-94396280-A-G
• chr5-94396280-A-T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001145678.3(KIAA0825):​c.3117T>G​(p.Ser1039Ser) 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. Synonymous variant affecting the same amino acid position (i.e. S1039S) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KIAA0825 NM_001145678.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 14 publications found

Genes affected

KIAA0825 (HGNC:28532): (KIAA0825)

KIAA0825 Gene-Disease associations (from GenCC):

• polydactyly, postaxial, type a10

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• postaxial polydactyly type A

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP7: Synonymous conserved (PhyloP=0.35 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145678.3. 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
	KIAA0825	NM_001145678.3	MANE Select	c.3117T>G	p.Ser1039Ser	synonymous	Exon 17 of 21	NP_001139150.1	A0A804HHT9
	KIAA0825	NM_001385712.1		c.3132T>G	p.Ser1044Ser	synonymous	Exon 18 of 22	NP_001372641.1	A0A994J718
	KIAA0825	NM_001388325.1		c.3132T>G	p.Ser1044Ser	synonymous	Exon 17 of 21	NP_001375254.1	A0A994J718

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0825	ENST00000682413.1	MANE Select	c.3117T>G	p.Ser1039Ser	synonymous	Exon 17 of 21	ENSP00000506760.1	A0A804HHT9
	KIAA0825	ENST00000703867.1		c.3132T>G	p.Ser1044Ser	synonymous	Exon 17 of 21	ENSP00000515512.1	A0A994J718
	KIAA0825	ENST00000513200.7	TSL:5	c.3117T>G	p.Ser1039Ser	synonymous	Exon 16 of 20	ENSP00000424618.2	Q8IV33-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 48

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	11
DANN	Benign	0.69
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs308207; hg19: chr5-93731985;