rs7764884

Variant names:

• chr6-7970307-G-A
• rs7764884
• ENST00000439343.2:n.372+56060C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-7970307-G-A
• chr6-7970307-G-C
• chr6-7970307-G-T

Variant summary

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

The ENST00000439343.2(BLOC1S5-TXNDC5):​n.372+56060C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,914 control chromosomes in the GnomAD database, including 21,920 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 0.53 (21920 hom., cov: 30)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 2 publications found

Genes affected

BLOC1S5-TXNDC5 (HGNC:42001): (BLOC1S5-TXNDC5 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring MUTED (muted homolog) and TXNDC5 (thioredoxin domain containing 5) genes on chromosome 6. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is unlikely to produce a protein product. [provided by RefSeq, Dec 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.422+56060C>T		intron_variant	Intron 4 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLOC1S5-TXNDC5	ENST00000439343.2	n.372+56060C>T		intron_variant	Intron 4 of 12	2		ENSP00000454697.1

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79849 AN: 151796 Hom.: 21894 Cov.: 30

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.526 AC: 79916 AN: 151914 Hom.: 21920 Cov.: 30 AF XY: 0.529 AC XY: 39256 AN XY: 74248

African (AFR) AF: 0.377 AC: 15606 AN: 41398

American (AMR) AF: 0.624 AC: 9537 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1872 AN: 3464

East Asian (EAS) AF: 0.786 AC: 4035 AN: 5136

South Asian (SAS) AF: 0.555 AC: 2666 AN: 4806

European-Finnish (FIN) AF: 0.585 AC: 6173 AN: 10560

Middle Eastern (MID) AF: 0.400 AC: 116 AN: 290

European-Non Finnish (NFE) AF: 0.563 AC: 38270 AN: 67962

Other (OTH) AF: 0.520 AC: 1099 AN: 2114

Alfa AF: 0.554 Hom.: 12659

Bravo AF: 0.525

Asia WGS AF: 0.644 AC: 2241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.80
DANN	Benign	0.80
PhyloP100		-0.083
Mutation Taster		=100/0	polymorphism (auto)

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: rs7764884; hg19: chr6-7970540;