rs6053733

Variant names:

• chr20-5834428-A-G
• rs6053733
• NM_152504.4:c.179-28596A>G

Your query was ambiguous. Multiple possible variants found:

• chr20-5834428-A-G
• chr20-5834428-A-T

Variant summary

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

The NM_152504.4(SHLD1):​c.179-28596A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,064 control chromosomes in the GnomAD database, including 9,382 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 0.34 (9382 hom., cov: 32)
• Consequence: SHLD1 NM_152504.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

Genes affected

SHLD1 (HGNC:26318): (shieldin complex subunit 1) Involved in negative regulation of double-strand break repair via homologous recombination; positive regulation of double-strand break repair via nonhomologous end joining; and positive regulation of isotype switching. Located in site of double-strand break. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHLD1	NM_152504.4	c.179-28596A>G		intron_variant	Intron 2 of 2	ENST00000303142.11	NP_689717.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SHLD1	ENST00000303142.11	c.179-28596A>G		intron_variant	Intron 2 of 2	1	NM_152504.4	ENSP00000305875.6
SHLD1	ENST00000442185.1	c.320-28596A>G		intron_variant	Intron 3 of 3	3		ENSP00000410534.1
SHLD1	ENST00000445603.1	c.179-28596A>G		intron_variant	Intron 3 of 3	3		ENSP00000399331.1

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52204 AN: 151946 Hom.: 9375 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.344 AC: 52239 AN: 152064 Hom.: 9382 Cov.: 32 AF XY: 0.346 AC XY: 25733 AN XY: 74330

African (AFR) AF: 0.427 AC: 17707 AN: 41486

American (AMR) AF: 0.339 AC: 5182 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3462

East Asian (EAS) AF: 0.498 AC: 2580 AN: 5182

South Asian (SAS) AF: 0.326 AC: 1569 AN: 4810

European-Finnish (FIN) AF: 0.331 AC: 3490 AN: 10556

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19899 AN: 67982

Other (OTH) AF: 0.314 AC: 663 AN: 2112

Alfa AF: 0.273 Hom.: 1648

Bravo AF: 0.347

Asia WGS AF: 0.398 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.5
DANN	Benign	0.76
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

Publications

LitVar

Other links and lift over

dbSNP: rs6053733; hg19: chr20-5815074;