chr7-150367777-C-T

Variant names:

• chr7-150367777-C-T
• rs6946097
• ENST00000488310.1:n.176+3301G>A

Variant summary

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

The ENST00000488310.1(REPIN1-AS1):​n.176+3301G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,060 control chromosomes in the GnomAD database, including 6,178 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 0.26 (6178 hom., cov: 32)
• Consequence: REPIN1-AS1 ENST00000488310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 9 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REPIN1-AS1	NR_183428.1		n.341+2920G>A		intron	N/A
	REPIN1-AS1	NR_183429.1		n.333+2928G>A		intron	N/A
	REPIN1-AS1	NR_183434.1		n.354+2928G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REPIN1-AS1	ENST00000488310.1	TSL:4	n.176+3301G>A		intron	N/A
	REPIN1-AS1	ENST00000728192.1		n.218+1309G>A		intron	N/A
	REPIN1-AS1	ENST00000728193.1		n.94+978G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39599 AN: 151942 Hom.: 6186 Cov.: 32

Gnomad AFR AF: 0.0969

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.260 AC: 39585 AN: 152060 Hom.: 6178 Cov.: 32 AF XY: 0.269 AC XY: 19989 AN XY: 74332

African (AFR) AF: 0.0968 AC: 4015 AN: 41488

American (AMR) AF: 0.209 AC: 3190 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3468

East Asian (EAS) AF: 0.455 AC: 2355 AN: 5178

South Asian (SAS) AF: 0.432 AC: 2086 AN: 4826

European-Finnish (FIN) AF: 0.393 AC: 4140 AN: 10532

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21367 AN: 67980

Other (OTH) AF: 0.246 AC: 518 AN: 2106

Alfa AF: 0.281 Hom.: 2989

Bravo AF: 0.236

Asia WGS AF: 0.404 AC: 1403 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.2
DANN	Benign	0.70
PhyloP100		0.0020
PromoterAI		-0.023	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6946097; hg19: chr7-150064866;