rs707937

Positions:

• chr6-31763237-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001039651.2(SAPCD1):​c.114+69C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,201,240 control chromosomes in the GnomAD database, including 32,610 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 0.26 (5661 hom., cov: 32)
  • Exomes 𝑓: 0.22 (26949 hom.)
• Consequence: SAPCD1 NM_001039651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

SAPCD1 (HGNC:13938): (suppressor APC domain containing 1)

MSH5-SAPCD1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAPCD1	NM_001039651.2	c.114+69C>G		intron_variant		ENST00000415669.4
MSH5-SAPCD1	NR_037846.1	n.3321+69C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAPCD1	ENST00000415669.4	c.114+69C>G		intron_variant		1	NM_001039651.2	P2
SAPCD1	ENST00000425424.4	c.114+69C>G		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39425 AN: 151994 Hom.: 5657 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.264

GnomAD4 exome AF: 0.217 AC: 227765 AN: 1049128 Hom.: 26949 Cov.: 13 AF XY: 0.217 AC XY: 114754 AN XY: 528438

Gnomad4 AFR exome AF: 0.332

Gnomad4 AMR exome AF: 0.348

Gnomad4 ASJ exome AF: 0.136

Gnomad4 EAS exome AF: 0.430

Gnomad4 SAS exome AF: 0.271

Gnomad4 FIN exome AF: 0.202

Gnomad4 NFE exome AF: 0.197

Gnomad4 OTH exome AF: 0.222

GnomAD4 genome AF: 0.259 AC: 39463 AN: 152112 Hom.: 5661 Cov.: 32 AF XY: 0.263 AC XY: 19566 AN XY: 74362

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.263

Alfa AF: 0.217 Hom.: 516

Bravo AF: 0.273

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.53
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs707937; hg19: chr6-31731014;