rs374194422

Variant names:

• chr7-118234776-C-A
• rs374194422
• NM_019644.4:c.370C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-118234776-C-A
• chr7-118234776-C-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.370C>A​(p.Arg124Ser) 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. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R124C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ANKRD7 NM_019644.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 1 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=0.05449158).

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.370C>A	p.Arg124Ser	missense	Exon 3 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.370C>A	p.Arg124Ser	missense	Exon 3 of 7	ENSP00000265224.4	Q92527-1
	ANKRD7	ENST00000417525.5	TSL:5	c.370C>A	p.Arg124Ser	missense	Exon 3 of 7	ENSP00000395595.2	C9JIJ7
	ANKRD7	ENST00000477532.5	TSL:5	c.-147C>A		5_prime_UTR	Exon 3 of 6	ENSP00000489121.1	A0A0U1RQQ7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000122 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.43
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	0.34
DANN	Benign	0.58
DEOGEN2	Benign	0.037	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.014	N
LIST_S2	Benign	0.16	T
M_CAP	Benign	0.0051	T
MetaRNN	Benign	0.054	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.53	N
PhyloP100		-0.080
PrimateAI	Benign	0.29	T
PROVEAN	Benign	0.26	N
REVEL	Benign	0.021
Sift	Benign	0.35	T
Sift4G	Benign	0.43	T
Polyphen		0.015	B
Vest4		0.15
MVP		0.40
MPC		0.31
ClinPred		0.12	T
GERP RS		-6.0
Varity_R		0.075
gMVP		0.45
Mutation Taster		=99/1	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: rs374194422; hg19: chr7-117874830;