7-77109274-C-T

Variant names:

• chr7-77109274-C-T
• rs3864639
• ENST00000764077.1:n.1122G>A

Variant summary

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

The ENST00000764077.1(ENSG00000291121):​n.1122G>A 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 0.835 in 152,174 control chromosomes in the GnomAD database, including 53,430 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 0.84 (53430 hom., cov: 31)
• Consequence: ENSG00000291121 ENST00000764077.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 7 publications found

Genes affected

ENSG00000291121 (HGNC:):

FAM185BP (HGNC:21813): (family with sequence similarity 185 member B, pseudogene)

DTX2P1-UPK3BP1-PMS2P11 (HGNC:42360): (DTX2P1-UPK3BP1-PMS2P11 readthrough, transcribed pseudogene) This locus represents naturally-occurring readthrough transcription spanning multiple pseudogenes: DTX2P1 (DTX2 pseudogene 1), UPK3BP1 (uroplakin 3B pseudogene 1), PMS2P11 (PMS1 homolog 2, mismatch repair system component pseudogene 11). Some transcripts may also extend to PMS2P9 (PMS1 homolog 2, mismatch repair system component pseudogene 9). The readthrough transcripts likely do not encode functional proteins. [provided by RefSeq, Jan 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM185BP	NR_146190.1	n.966+664G>A		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291121	ENST00000764077.1	n.1122G>A		non_coding_transcript_exon_variant	Exon 5 of 5
FAM185BP	ENST00000443595.2	n.793+664G>A		intron_variant	Intron 4 of 6	6
DTX2P1-UPK3BP1-PMS2P11	ENST00000579700.2	n.1226-58384C>T		intron_variant	Intron 9 of 10	2

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126961 AN: 152058 Hom.: 53374 Cov.: 31

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.835 AC: 127078 AN: 152174 Hom.: 53430 Cov.: 31 AF XY: 0.837 AC XY: 62288 AN XY: 74386

African (AFR) AF: 0.937 AC: 38932 AN: 41534

American (AMR) AF: 0.834 AC: 12746 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2742 AN: 3468

East Asian (EAS) AF: 0.786 AC: 4073 AN: 5182

South Asian (SAS) AF: 0.747 AC: 3602 AN: 4822

European-Finnish (FIN) AF: 0.870 AC: 9221 AN: 10598

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53257 AN: 67966

Other (OTH) AF: 0.823 AC: 1739 AN: 2114

Alfa AF: 0.822 Hom.: 64139

Bravo AF: 0.834

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.8
DANN	Benign	0.87
PhyloP100		0.36
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs3864639; hg19: chr7-76738591;