chr11-9738166-T-G

Variant names:

• chr11-9738166-T-G
• rs93138
• NM_015055.4:c.1081-47T>G

Variant summary

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

The NM_015055.4(SWAP70):​c.1081-47T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 1,388,812 control chromosomes in the GnomAD database, including 224,917 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 0.56 (23762 hom., cov: 33)
  • Exomes 𝑓: 0.57 (201155 hom.)
• Consequence: SWAP70 NM_015055.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

SWAP70 (HGNC:17070): (switching B cell complex subunit SWAP70) Enables cadherin binding activity. Predicted to be involved in regulation of actin polymerization or depolymerization. Predicted to act upstream of or within isotype switching. Located in actin cytoskeleton; cytoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SWAP70	NM_015055.4	c.1081-47T>G		intron_variant	Intron 7 of 11	ENST00000318950.11	NP_055870.2
SWAP70	NM_001297714.2	c.907-47T>G		intron_variant	Intron 6 of 10		NP_001284643.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SWAP70	ENST00000318950.11	c.1081-47T>G		intron_variant	Intron 7 of 11	1	NM_015055.4	ENSP00000315630.6

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84466 AN: 151960 Hom.: 23758 Cov.: 33

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.589

GnomAD3 exomes AF: 0.572 AC: 106093 AN: 185626 Hom.: 30756 AF XY: 0.572 AC XY: 56750 AN XY: 99182

Gnomad AFR exome AF: 0.495

Gnomad AMR exome AF: 0.595

Gnomad ASJ exome AF: 0.659

Gnomad EAS exome AF: 0.399

Gnomad SAS exome AF: 0.503

Gnomad FIN exome AF: 0.682

Gnomad NFE exome AF: 0.588

Gnomad OTH exome AF: 0.596

GnomAD4 exome AF: 0.567 AC: 700877 AN: 1236734 Hom.: 201155 Cov.: 15 AF XY: 0.566 AC XY: 351168 AN XY: 620154

Gnomad4 AFR exome AF: 0.485

Gnomad4 AMR exome AF: 0.585

Gnomad4 ASJ exome AF: 0.652

Gnomad4 EAS exome AF: 0.385

Gnomad4 SAS exome AF: 0.503

Gnomad4 FIN exome AF: 0.677

Gnomad4 NFE exome AF: 0.572

Gnomad4 OTH exome AF: 0.570

GnomAD4 genome AF: 0.556 AC: 84483 AN: 152078 Hom.: 23762 Cov.: 33 AF XY: 0.556 AC XY: 41358 AN XY: 74334

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.658

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.590

Alfa AF: 0.585 Hom.: 36835

Bravo AF: 0.546

Asia WGS AF: 0.442 AC: 1541 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	3.7
DANN	Benign	0.73

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: rs93138; hg19: chr11-9759713; COSMIC: COSV59662666;