chr2-7062365-T-G

Variant names:

• chr2-7062365-T-G
• rs309271
• ENST00000415520.6:n.642A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000415520.6(ENSG00000223884):​n.642A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,908 control chromosomes in the GnomAD database, including 6,772 homozygotes. 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: 𝑓 0.27 (6772 hom., cov: 31)
• Consequence: ENSG00000223884 ENST00000415520.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 1 publications found

Genes affected

ENSG00000223884 (HGNC:):

RNF144A (HGNC:20457): (ring finger protein 144A) This gene encodes a member of a family of RING finger domain-containing E3 ubiquitin ligases that also includes parkin and parc. The expression of this gene is induced by DNA damage. The encoded protein interacts with the cytoplasmic DNA-dependent protein kinase, catalytic subunit (DNA-PKcs) and promotes its degradation through ubiquitination. The orthologous mouse protein has been shown to interact with a ubiquitin-conjugating enzyme involved in embryonic development. [provided by RefSeq, Mar 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415520.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF144A	NM_001349181.2		c.748-10797T>G		intron	N/A	NP_001336110.1
	RNF144A	NM_001349185.2		c.748-5851T>G		intron	N/A	NP_001336114.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223884	ENST00000415520.6	TSL:4	n.642A>C		non_coding_transcript_exon	Exon 4 of 5
	ENSG00000223884	ENST00000649356.2		n.1309A>C		non_coding_transcript_exon	Exon 6 of 6
	ENSG00000223884	ENST00000777551.1		n.996A>C		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41360 AN: 151796 Hom.: 6758 Cov.: 31

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.241

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.272 AC: 41392 AN: 151908 Hom.: 6772 Cov.: 31 AF XY: 0.278 AC XY: 20603 AN XY: 74204

African (AFR) AF: 0.0889 AC: 3684 AN: 41462

American (AMR) AF: 0.381 AC: 5824 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 998 AN: 3470

East Asian (EAS) AF: 0.298 AC: 1537 AN: 5164

South Asian (SAS) AF: 0.427 AC: 2044 AN: 4788

European-Finnish (FIN) AF: 0.341 AC: 3585 AN: 10506

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22849 AN: 67936

Other (OTH) AF: 0.248 AC: 521 AN: 2102

Alfa AF: 0.306 Hom.: 16100

Bravo AF: 0.268

Asia WGS AF: 0.378 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.59
DANN	Benign	0.46
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs309271; hg19: chr2-7202496;