rs1699236

Variant names:

• chr20-5861822-G-A
• rs1699236
• NM_152504.4:c.179-1202G>A

Variant summary

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

The NM_152504.4(SHLD1):​c.179-1202G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 152,078 control chromosomes in the GnomAD database, including 40,297 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 0.73 (40297 hom., cov: 31)
• Consequence: SHLD1 NM_152504.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 3 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHLD1	NM_152504.4	c.179-1202G>A		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.179-1202G>A		intron_variant	Intron 2 of 2	1	NM_152504.4	ENSP00000305875.6
SHLD1	ENST00000442185.1	c.320-1202G>A		intron_variant	Intron 3 of 3	3		ENSP00000410534.1
SHLD1	ENST00000445603.1	c.179-1202G>A		intron_variant	Intron 3 of 3	3		ENSP00000399331.1

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110390 AN: 151960 Hom.: 40268 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.726 AC: 110474 AN: 152078 Hom.: 40297 Cov.: 31 AF XY: 0.724 AC XY: 53811 AN XY: 74336

African (AFR) AF: 0.792 AC: 32847 AN: 41470

American (AMR) AF: 0.743 AC: 11364 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2493 AN: 3472

East Asian (EAS) AF: 0.760 AC: 3926 AN: 5168

South Asian (SAS) AF: 0.659 AC: 3174 AN: 4820

European-Finnish (FIN) AF: 0.655 AC: 6917 AN: 10564

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47419 AN: 67982

Other (OTH) AF: 0.720 AC: 1520 AN: 2110

Alfa AF: 0.701 Hom.: 19076

Bravo AF: 0.739

Asia WGS AF: 0.723 AC: 2514 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	4.4
DANN	Benign	0.64
PhyloP100		0.14
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: rs1699236; hg19: chr20-5842468;