NM_019644.4:c.610C>T

Variant names:

• chr7-118236824-C-T
• rs1809738407
• NM_019644.4:c.610C>T

Variant summary

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

The NM_019644.4(ANKRD7):​c.610C>T​(p.Pro204Ser) 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 Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ANKRD7 NM_019644.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.793
• Publications: 0 publications found

Genes affected

ANKRD7 (HGNC:18588): (ankyrin repeat domain 7) Predicted to act upstream of or within blastocyst hatching. Located in centrosome and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.061571836).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019644.4. 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
	ANKRD7	NM_019644.4	MANE Select	c.610C>T	p.Pro204Ser	missense	Exon 5 of 7	NP_062618.2	Q92527-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD7	ENST00000265224.9	TSL:1 MANE Select	c.610C>T	p.Pro204Ser	missense	Exon 5 of 7	ENSP00000265224.4	Q92527-1
	ANKRD7	ENST00000417525.5	TSL:5	c.610C>T	p.Pro204Ser	missense	Exon 5 of 7	ENSP00000395595.2	C9JIJ7
	ANKRD7	ENST00000477532.5	TSL:5	c.94C>T	p.Pro32Ser	missense	Exon 5 of 6	ENSP00000489121.1	A0A0U1RQQ7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Uncertain significance

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	0.12
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	0.78
DANN	Benign	0.18
DEOGEN2	Benign	0.0057	T
Eigen	Benign	-1.7
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.025	N
LIST_S2	Benign	0.22	T
M_CAP	Benign	0.0068	T
MetaRNN	Benign	0.062	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.42	N
PhyloP100		0.79
PrimateAI	Benign	0.34	T
PROVEAN	Benign	0.64	N
REVEL	Benign	0.013
Sift	Benign	0.40	T
Sift4G	Benign	0.64	T
Polyphen		0.0	B
Vest4		0.14
MutPred		0.35		Loss of catalytic residue at P203 (P = 0.0151)
MVP		0.072
MPC		0.27
ClinPred		0.046	T
GERP RS		-0.86
Varity_R		0.018
gMVP		0.34
Mutation Taster		=93/7	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: rs1809738407; hg19: chr7-117876878; COSMIC: COSV54553966; COSMIC: COSV54553966;