chr7-150364445-C-G

Variant names:

• chr7-150364445-C-G
• rs7800196
• ENST00000488310.1:n.177-268G>C

Variant summary

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

The ENST00000488310.1(REPIN1-AS1):​n.177-268G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,866 control chromosomes in the GnomAD database, including 7,977 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 0.32 (7977 hom., cov: 32)
• Consequence: REPIN1-AS1 ENST00000488310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.628
• Publications: 5 publications found

Genes affected

REPIN1-AS1 (HGNC:41201): (REPIN1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000488310.1. 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
	REPIN1-AS1	NR_183428.1		n.342-379G>C		intron	N/A
	REPIN1-AS1	NR_183429.1		n.334-268G>C		intron	N/A
	REPIN1-AS1	NR_183434.1		n.355-268G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REPIN1-AS1	ENST00000488310.1	TSL:4	n.177-268G>C		intron	N/A
	REPIN1-AS1	ENST00000728192.1		n.219-268G>C		intron	N/A
	REPIN1-AS1	ENST00000728193.1		n.95-379G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48632 AN: 151746 Hom.: 7961 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.321 AC: 48687 AN: 151866 Hom.: 7977 Cov.: 32 AF XY: 0.327 AC XY: 24249 AN XY: 74246

African (AFR) AF: 0.361 AC: 14984 AN: 41464

American (AMR) AF: 0.233 AC: 3553 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1178 AN: 3456

East Asian (EAS) AF: 0.470 AC: 2406 AN: 5124

South Asian (SAS) AF: 0.410 AC: 1973 AN: 4818

European-Finnish (FIN) AF: 0.358 AC: 3781 AN: 10552

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19746 AN: 67876

Other (OTH) AF: 0.291 AC: 614 AN: 2108

Alfa AF: 0.319 Hom.: 948

Bravo AF: 0.312

Asia WGS AF: 0.420 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.40
PhyloP100		0.63

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7800196;

hg19: chr7-150061534;