rs197119

Variant names:

• chr6-7976512-G-A
• rs197119
• ENST00000439343.2:n.372+49855C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-7976512-G-A
• chr6-7976512-G-C
• chr6-7976512-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+49855C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,106 control chromosomes in the GnomAD database, including 36,455 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 0.69 (36455 hom., cov: 32)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.422+49855C>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+49855C>T		intron_variant	Intron 4 of 12	2		ENSP00000454697.1

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104731 AN: 151988 Hom.: 36419 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.689 AC: 104820 AN: 152106 Hom.: 36455 Cov.: 32 AF XY: 0.691 AC XY: 51426 AN XY: 74374

African (AFR) AF: 0.754 AC: 31300 AN: 41496

American (AMR) AF: 0.705 AC: 10784 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2312 AN: 3472

East Asian (EAS) AF: 0.820 AC: 4245 AN: 5174

South Asian (SAS) AF: 0.580 AC: 2794 AN: 4814

European-Finnish (FIN) AF: 0.690 AC: 7293 AN: 10574

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43924 AN: 67970

Other (OTH) AF: 0.669 AC: 1412 AN: 2110

Alfa AF: 0.667 Hom.: 14744

Bravo AF: 0.698

Asia WGS AF: 0.709 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.77
DANN	Benign	0.71
PhyloP100		-0.71
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: rs197119; hg19: chr6-7976745;